[1] "ofn"        "-oTSTES-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/STES-TP/15090071/STES-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/15101919/transformed.cor.cli.txt"

nPatients in clinical file=612, in cluster file=625, common to both=609
[1]  82 609
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               78               531 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               78               531 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              161               448 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              161               448 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              131               478 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              131               478 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              106               503 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              106               503 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               81               528 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               81               528 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              163               446 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              163               446 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               36               573 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               36               573 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               31               578 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               31               578 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              167               442 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              167               442 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               62               547 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               62               547 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              113               496 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              113               496 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               96               513 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               96               513 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              299               310 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              299               310 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              251               358 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              251               358 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              243               366 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              243               366 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              328               281 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              328               281 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               73               536 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               73               536 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              104               505 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              104               505 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               133                476 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               133                476 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                97                512 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                97                512 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                98                511 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                98                511 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               103                506 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               103                506 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               142                467 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               142                467 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               112                497 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               112                497 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               192                417 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               192                417 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                71                538 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                71                538 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                64                545 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                64                545 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                95                514 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                95                514 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                83                526 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                83                526 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                59                550 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                59                550 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               101                508 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               101                508 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               134                475 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               134                475 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                81                528 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                81                528 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                80                529 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                80                529 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               114                495 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               114                495 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               340                269 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               340                269 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               387                222 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               387                222 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                575 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                575 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                62                547 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                62                547 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               69               540 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               69               540 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               87               522 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               87               522 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               91               518 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               91               518 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               45               564 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               45               564 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               38               571 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               38               571 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               51               558 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               51               558 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              177               432 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              177               432 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               89               520 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               89               520 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              263               346 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              263               346 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              247               362 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              247               362 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              110               499 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              110               499 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              187               422 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              187               422 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               90               519 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               90               519 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              107               502 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              107               502 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               33               576 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               33               576 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               51               558 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               51               558 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              146               463 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              146               463 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               56               553 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               56               553 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              241               368 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              241               368 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              169               440 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              169               440 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               111                498 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               111                498 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               111                498 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               111                498 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               113                496 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               113                496 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               114                495 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               114                495 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                92                517 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                92                517 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                79                530 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                79                530 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                97                512 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                97                512 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               155                454 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               155                454 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               142                467 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               142                467 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               154                455 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               154                455 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               164                445 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               164                445 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               229                380 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               229                380 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                97                512 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                97                512 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               181                428 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               181                428 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               248                361 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               248                361 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               172                437 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               172                437 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               132                477 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               132                477 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                40                569 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                40                569 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                601 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                601 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               279                330 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               279                330 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               212                397 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               212                397 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              116               493 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              116               493 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               93               516 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               93               516 
[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] "NUMBER_PACK_YEARS_SMOKED"              
[17] "COMPLETENESS_OF_RESECTION"             
[18] "NUMBER_OF_LYMPH_NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 609 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=197,	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=323,	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=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=6,	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:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH_NUMBER':	nDistinctValues=34,	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 609 columns, 1 survival variables, and 13 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] "NUMBER_PACK_YEARS_SMOKED"              
[10] "COMPLETENESS_OF_RESECTION"             
[11] "NUMBER_OF_LYMPH_NODES"                 
[12] "RACE"                                  
[13] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=56, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  52 126 280 124 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   53   126   280   124 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  52 126 280 124 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   53   126   280   124 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
200 182  96  97 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
200 182  96  97 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
200 182  96  97 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
200 182  96  97 
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
NUMBER_PACK_YEARS_SMOKED, nv=45, binary=FALSE, numeric=TRUE
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    37  33
  1P GAIN WILD-TYPE 317 188
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               70               505 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               33               188 
$`1P GAIN MUTATED`
TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A93E TCGA-L5-A4OM 
       13.94        20.09        17.03         4.67        25.22        47.93 
TCGA-L5-A4ON TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       18.35         7.43         0.36         3.95         3.02         2.66 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49X 
       13.22        13.41        10.36         5.92        10.45         0.10 
TCGA-LN-A5U6 TCGA-LN-A9FO TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-V5-A7RC 
       12.33         0.13        29.59        15.78        12.69         3.42 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-BR-4267 TCGA-BR-7717 
       22.82         8.12         2.10        19.73         6.18        18.15 
TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8588 
        3.45        12.95         0.26         5.39        25.18        12.79 
TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-CD-A48A TCGA-CG-4436 TCGA-D7-6521 
        8.22         0.72        13.51        12.43         7.99        18.54 
TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       16.44         2.96         7.99         5.52        26.47         5.92 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-A6RI 
       25.81        11.77         8.98         6.25        12.95        18.38 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-KB-A6F7 TCGA-R5-A7ZR TCGA-RD-A7C1 
        1.41         6.44         6.74        60.56         6.08        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PK 
      115.69         8.94        48.79        18.48        35.24        17.85 
TCGA-VQ-A8PZ TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A 
       65.16        42.54        18.41        32.94 

$`1P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       30.25         0.30         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP 
        4.70        32.61        19.99        21.01         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE 
        6.94         8.71         2.60        25.12         7.40        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       46.09        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35         0.10        13.25        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.23        12.03        13.18        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        14.70         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
       53.95         9.30         2.89         1.45         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       18.81        19.96        12.43         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-5816 
        9.17        15.91        10.16         3.42         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        15.42        28.01        15.32        28.73        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-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-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       14.79        15.85         3.72         9.21        20.22         1.12 
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-8690 
       11.54        15.81        16.44         9.86        15.68        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-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-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-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-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-D7-6820 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-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-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        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-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-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
       13.58         0.56         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-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-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       22.75        21.37        29.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        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-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39         5.36         5.19        13.08        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-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         5.13       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92         5.46        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-A8PJ TCGA-VQ-A8PM 
       16.31        22.19         2.50        12.79         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-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-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        22.68         1.71        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-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-A94T TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        22.09        40.08        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 
TCGA-ZQ-A9CR 
        0.79 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              0.1               0.0 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           115.69            122.30 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            12.56             12.79 
[1] "0.1 - 115.7 (12.6)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         2        3        7        2         8        13
  1P GAIN WILD-TYPE       9       16       41       30        69        71
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           3         10         10          7        2
  1P GAIN WILD-TYPE        26         87         62         41       49
                   vv
clus                STAGE IVA
  1P GAIN MUTATED           2
  1P GAIN WILD-TYPE         2
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  2                 9
  STAGE IA                 3                16
  STAGE IB                 7                41
  STAGE II                 2                30
  STAGE IIA                8                69
  STAGE IIB               13                71
  STAGE III                3                26
  STAGE IIIA              10                87
  STAGE IIIB              10                62
  STAGE IIIC               7                41
  STAGE IV                 2                49
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1P GAIN MUTATED      12  15  37   9
  1P GAIN WILD-TYPE    41 111 243 115
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1              12                41
  T2                 15               111
  T3                 37               243
  T4                  9               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
  1P GAIN MUTATED    25  22  12  11
  1P GAIN WILD-TYPE 175 160  84  86
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              25               175
  N1              22               160
  N2              12                84
  N3              11                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"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    65   2
  1P GAIN WILD-TYPE 448  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     65    2
  1P GAIN WILD-TYPE  448   37
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              65               448
  1               2                37
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    17  61
  1P GAIN WILD-TYPE 165 366
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     17   61
  1P GAIN WILD-TYPE  165  366
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              17               165
  MALE                61               366
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1P GAIN MUTATED                                       5
  1P GAIN WILD-TYPE                                    66
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                       21
  1P GAIN WILD-TYPE                                                    141
                   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                                           5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         21
  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                                            66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          141
  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  78
  1P GAIN WILD-TYPE   6 525
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   78
  1P GAIN WILD-TYPE    6  525
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                 6
  YES              78               525
[1] 2 2
[1] FALSE
D1V10, continuous
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    38   3   0   5
  1P GAIN WILD-TYPE 309  15  19  20
D1V11, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              38               309
  R1               3                15
  R2               0                19
  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"
D1V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED      18                         3
  1P GAIN WILD-TYPE   111                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           0    53
  1P GAIN WILD-TYPE                                         1   332
D1V13, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                                  18               111
  BLACK OR AFRICAN AMERICAN                               3                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  53               332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  54
  1P GAIN WILD-TYPE   6 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   54
  1P GAIN WILD-TYPE    6  340
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              54               340
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    85  65
  1Q GAIN WILD-TYPE 269 156
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              150               425 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               65               156 
$`1Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 
       13.94         8.94        20.09         0.85        20.12        18.64 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A93D 
       17.03         0.79        23.41        12.82         4.67        31.56 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       25.22         0.30         3.68        32.61        47.93        18.35 
TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        4.90         7.43         0.36         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS 
       55.50         2.66        12.92        13.22         5.49        13.41 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       10.36         5.92        10.45        15.35         0.10         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW 
       12.49        12.76        13.22         4.47        12.33        12.00 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8WG 
       13.18         0.13        14.70        29.59        15.78        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA4D 
       20.38         3.42        22.82         8.12        28.11        46.19 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-BR-4267 
       15.91        10.16         2.10        19.73        11.01         6.18 
TCGA-BR-6705 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8295 
       25.61        18.15        28.73         3.45        12.95         2.20 
TCGA-BR-8360 TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        6.18        14.04         0.26         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A452 
       20.22         1.12        12.79        15.81         8.22         7.53 
TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-CD-8524 TCGA-CD-8530 
        0.72        12.82        13.51        20.42         0.07         0.16 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CG-4436 TCGA-CG-4438 
        0.13         0.13        11.61         6.58         7.99        54.08 
TCGA-CG-4460 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 
       21.99        12.66        11.93        18.54        17.19        10.26 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       12.79        10.55        11.31        12.33        24.72        19.50 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       16.44        11.31         2.96         0.62         7.99        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
        3.48        14.07        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
        5.92        14.27        14.17        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-A6RO TCGA-IN-A6RP 
        0.10         6.25        12.95         3.45         1.41         6.44 
TCGA-KB-A6F7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
       60.56        18.21         6.08        16.67       115.69         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PJ 
       35.61        48.79         5.46        18.48        35.24         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91S TCGA-VQ-A92D 
       17.85        14.33        65.16        36.69        22.68        64.18 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A 
       21.04        42.54        11.24        22.09        18.41        32.94 

$`1Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       16.24         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A6QS 
       20.78         2.63         3.88         9.30         0.53         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J 
       23.18        24.03         6.28         3.16        30.25         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
        8.94        24.00         4.70        19.99        21.01         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NG TCGA-L5-A8NI 
        6.94         8.71         2.60        25.12        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT 
       16.47        13.55         7.76        21.37         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        52.57        46.09        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 
        0.10        13.15        13.25        12.46        12.59        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U7 
       22.39         0.10        15.52        11.54        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       10.52        12.23        12.03        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59         5.06         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        9.30         2.89         1.45         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        4.80        15.35         9.27         4.44        18.81        19.96 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.43         1.55        18.31        30.71        18.18        42.87 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-5816 
       15.06        11.24         9.17         3.42         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        18.35        30.90         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        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-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.01        15.32        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-8289 TCGA-BR-8291 TCGA-BR-8296 
       20.55         8.05         0.56         2.66        16.31        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40        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-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       14.79        15.85         3.72        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ 
       15.68        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-A4J2 
        1.48        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.53         0.66        19.36         0.46        20.65         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-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 
           12.775            12.760 
[1] "0.1 - 115.7 (12.8)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         3        6       14        7        18        23
  1Q GAIN WILD-TYPE       8       13       34       25        59        61
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           9         25         19         12       10
  1Q GAIN WILD-TYPE        20         72         53         36       41
                   vv
clus                STAGE IVA
  1Q GAIN MUTATED           3
  1Q GAIN WILD-TYPE         1
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  3                 8
  STAGE IA                 6                13
  STAGE IB                14                34
  STAGE II                 7                25
  STAGE IIA               18                59
  STAGE IIB               23                61
  STAGE III                9                20
  STAGE IIIA              25                72
  STAGE IIIB              19                53
  STAGE IIIC              12                36
  STAGE IV                10                41
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1Q GAIN MUTATED      21  33  75  26
  1Q GAIN WILD-TYPE    32  93 205  98
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              21                32
  T2                 33                93
  T3                 75               205
  T4                 26                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
  1Q GAIN MUTATED    53  46  27  24
  1Q GAIN WILD-TYPE 147 136  69  73
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              53               147
  N1              46               136
  N2              27                69
  N3              24                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"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   131  11
  1Q GAIN WILD-TYPE 382  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    131   11
  1Q GAIN WILD-TYPE  382   28
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             131               382
  1              11                28
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    38 123
  1Q GAIN WILD-TYPE 144 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     38  123
  1Q GAIN WILD-TYPE  144  304
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              38               144
  MALE               123               304
[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                                                       36
  1Q GAIN WILD-TYPE                                                    126
                   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)                         36
  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)                          126
  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     2 159
  1Q GAIN WILD-TYPE   4 444
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2  159
  1Q GAIN WILD-TYPE    4  444
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                2                 4
  YES             159               444
[1] 2 2
[1] FALSE
D2V10, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    79   5   3   7
  1Q GAIN WILD-TYPE 268  13  16  18
D2V11, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              79               268
  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"
D2V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED      40                         7
  1Q GAIN WILD-TYPE    89                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           0   103
  1Q GAIN WILD-TYPE                                         1   282
D2V13, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                                  40                89
  BLACK OR AFRICAN AMERICAN                               7                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 103               282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     1 112
  1Q GAIN WILD-TYPE   6 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1  112
  1Q GAIN WILD-TYPE    6  282
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO             112               282
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    77  48
  2P GAIN WILD-TYPE 277 173
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              125               450 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               48               173 
$`2P GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RF TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A8O2 
       13.94         8.94         6.21        18.64        23.41         4.67 
TCGA-JY-A6FA TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
       44.75        25.22         4.31         3.68        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y 
       18.35         3.32         3.16         7.13         2.60         0.36 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49Y 
       52.57        10.36         5.92         0.10        13.15        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       12.59        12.49        12.76        12.59         0.10        12.33 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.33        25.25        12.00         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG 
       14.70         7.04        29.59         6.35        53.95        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU 
       20.38         3.42         4.80        15.35        19.96        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR 
        8.12        28.11        30.71        46.19        11.24        10.16 
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-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03         0.79        12.82         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       24.03         6.28         3.16        30.25         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ 
       24.00         4.70        19.99        21.01         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       58.59         4.90        29.00         7.43         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        46.09        10.45        12.66        12.43        13.41 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A5 TCGA-LN-A4A8 
       15.35         0.10        13.25         0.10        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       11.54        13.22         4.47        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6Y2 
       13.18         0.13        33.11         5.16         7.82         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.89         1.45         7.00        20.02         5.29 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        18.81        22.82        12.43         1.55 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       18.18        42.87        15.06         9.17        15.91         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-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-6565 
       13.87        13.68        19.33        39.12        26.10         9.17 
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-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01        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-8078 
       12.76        18.71        17.49        14.43        11.44        12.26 
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-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-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-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-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-A4IZ 
        7.53         6.08        22.26        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-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        3.25         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-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-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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44         9.76         2.96         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-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-A4G3 
       14.27        12.59        11.41        12.10        10.62         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20         3.25        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
        0.10         6.51         6.25        10.19         0.26        19.36 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
        9.67         8.88         8.81        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR 
       18.38         5.36         5.19        13.08         6.44         6.51 
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-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73        45.67         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-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-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.50         2.70         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-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-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        22.68        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-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
        5.72        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       18.41        28.41        17.13        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 
            12.79             12.71 
[1] "0.1 - 79.1 (12.8)"  "0.0 - 122.3 (12.7)"
[1] "hr=" "1"  
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         1        8        9        8        16        22
  2P GAIN WILD-TYPE      10       11       39       24        61        62
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           7         14         13         11        8
  2P GAIN WILD-TYPE        22         83         59         37       43
                   vv
clus                STAGE IVA
  2P GAIN MUTATED           1
  2P GAIN WILD-TYPE         3
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                10
  STAGE IA                 8                11
  STAGE IB                 9                39
  STAGE II                 8                24
  STAGE IIA               16                61
  STAGE IIB               22                62
  STAGE III                7                22
  STAGE IIIA              14                83
  STAGE IIIB              13                59
  STAGE IIIC              11                37
  STAGE IV                 8                43
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2P GAIN MUTATED      18  21  62  19
  2P GAIN WILD-TYPE    35 105 218 105
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              18                35
  T2                 21               105
  T3                 62               218
  T4                 19               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
  2P GAIN MUTATED    46  34  17  22
  2P GAIN WILD-TYPE 154 148  79  75
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              46               154
  N1              34               148
  N2              17                79
  N3              22                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"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   101   7
  2P GAIN WILD-TYPE 412  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    101    7
  2P GAIN WILD-TYPE  412   32
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0             101               412
  1               7                32
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    35  96
  2P GAIN WILD-TYPE 147 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     35   96
  2P GAIN WILD-TYPE  147  331
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              35               147
  MALE                96               331
[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     0 131
  2P GAIN WILD-TYPE   6 472
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0  131
  2P GAIN WILD-TYPE    6  472
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                0                 6
  YES             131               472
[1] 2 2
[1] FALSE
D3V10, continuous
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    66   1   3   2
  2P GAIN WILD-TYPE 281  17  16  23
D3V11, 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"
D3V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED      38                         3
  2P GAIN WILD-TYPE    91                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           0    77
  2P GAIN WILD-TYPE                                         1   308
D3V13, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                                  38                91
  BLACK OR AFRICAN AMERICAN                               3                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  77               308
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1  86
  2P GAIN WILD-TYPE   6 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1   86
  2P GAIN WILD-TYPE    6  308
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              86               308
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    61  39
  2Q GAIN WILD-TYPE 293 182
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              100               475 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               39               182 
$`2Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RF TCGA-IG-A5S3 TCGA-JY-A6FA TCGA-JY-A93E 
       13.94         8.94         6.21        23.41        44.75        25.22 
TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OW TCGA-L5-A88V 
        4.31         3.68        32.61         3.32         7.13         2.60 
TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A4A1 
        0.36        55.50        52.57         5.92         0.10        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.49        12.59         0.10        12.33        25.25        12.00 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP 
        6.35        53.95        12.69         3.42         4.80        19.96 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-B7-A5TJ TCGA-BR-6456 
       18.31        28.11        46.19        10.16        11.01        17.29 
TCGA-BR-6566 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8077 
       32.78         9.21        35.24        15.42        18.15         0.69 
TCGA-BR-8080 TCGA-BR-8295 TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-A4CS 
        9.60         2.20        13.08         5.39         9.21         1.48 
TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-CD-5801 TCGA-CD-8524 
       12.89         0.66        13.51        20.42        13.18         0.07 
TCGA-CD-A48C TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5727 
       11.61        21.99        12.00        36.00        12.03        79.07 
TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-EQ-8122 TCGA-F1-6875 
       18.54        15.98        16.44        11.24         7.99        72.23 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.76        24.30        12.30        25.81         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       23.84        12.30         3.45         6.74        12.59         5.56 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH 
        5.56        37.64         9.86        35.24        22.19        12.79 
TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-AA6A TCGA-VQ-AA6B 
       17.85        20.81         1.71        64.18        32.94        29.98 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        10.62         0.79 

$`2Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB 
       14.86         4.67        14.50        12.16       122.10        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        0.30         8.94        24.00         4.70        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        4.90        29.00         7.43         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.40         3.95         3.02         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW 
       21.37         8.71        13.41        27.12        83.24        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       10.36        10.45        12.66        12.43        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
       15.35         0.10        13.25         0.10        12.46        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        5.16         7.04         9.30        15.78         2.89         1.45 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.02        20.38         5.29        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
        4.44        18.81        22.82        12.43         1.55         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        42.87        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       15.91         3.42         2.10         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56         9.47         9.44         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-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-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-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-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       22.26        13.41        13.51         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.53        12.82        19.36         0.46        20.65         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-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.30         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-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
        0.10         3.42         9.34        11.31        12.43         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-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-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6817 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-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-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-A4SO TCGA-F1-6874 
        4.34         7.40         7.13         0.62        16.24        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-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-A4G3 
       12.59        14.17        11.41        12.10        10.62         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        0.26        19.36         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-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
       13.08         1.41         6.44         6.51         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-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-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-A8E3 
       48.79         5.46        13.25        13.02        18.48        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-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.50         2.70         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-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-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        22.68        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-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
        5.72        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        40.08        28.41        17.13        54.12        26.04 
TCGA-VQ-AA6K 
       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 
            12.59             12.82 
[1] "0.1 - 79.1 (12.6)"  "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         1        5        7        6        12        20
  2Q GAIN WILD-TYPE      10       14       41       26        65        64
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           5          9         12          8        7
  2Q GAIN WILD-TYPE        24         88         60         40       44
                   vv
clus                STAGE IVA
  2Q GAIN MUTATED           1
  2Q GAIN WILD-TYPE         3
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  1                10
  STAGE IA                 5                14
  STAGE IB                 7                41
  STAGE II                 6                26
  STAGE IIA               12                65
  STAGE IIB               20                64
  STAGE III                5                24
  STAGE IIIA               9                88
  STAGE IIIB              12                60
  STAGE IIIC               8                40
  STAGE IV                 7                44
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2Q GAIN MUTATED      13  19  48  16
  2Q GAIN WILD-TYPE    40 107 232 108
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              13                40
  T2                 19               107
  T3                 48               232
  T4                 16               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
  2Q GAIN MUTATED    34  30  12  18
  2Q GAIN WILD-TYPE 166 152  84  79
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              34               166
  N1              30               152
  N2              12                84
  N3              18                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"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    82   6
  2Q GAIN WILD-TYPE 431  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     82    6
  2Q GAIN WILD-TYPE  431   33
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              82               431
  1               6                33
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    28  78
  2Q GAIN WILD-TYPE 154 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     28   78
  2Q GAIN WILD-TYPE  154  349
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              28               154
  MALE                78               349
[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     0 106
  2Q GAIN WILD-TYPE   6 497
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0  106
  2Q GAIN WILD-TYPE    6  497
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                0                 6
  YES             106               497
[1] 2 2
[1] FALSE
D4V10, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    55   1   3   2
  2Q GAIN WILD-TYPE 292  17  16  23
D4V11, 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"
D4V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED      26                         3
  2Q GAIN WILD-TYPE   103                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           0    65
  2Q GAIN WILD-TYPE                                         1   320
D4V13, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                                  26               103
  BLACK OR AFRICAN AMERICAN                               3                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  65               320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     1  69
  2Q GAIN WILD-TYPE   6 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   69
  2Q GAIN WILD-TYPE    6  325
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              69               325
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    45  31
  3P GAIN WILD-TYPE 309 190
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               76               499 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               31               190 
$`3P GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-JY-A93C 
       31.27        16.24         7.69        33.27        18.64        23.18 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A891 
       25.22         0.30         4.31        47.93         3.16         3.95 
TCGA-L5-A8NE TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R 
       55.50        27.12        52.57        10.36        10.45         0.10 
TCGA-LN-A4A1 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-AASW 
       12.59         5.16         5.06        53.95        12.69         9.27 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-AA7B TCGA-ZR-A9CJ TCGA-BR-4267 TCGA-BR-6452 
       22.82        12.43        11.24        19.73         6.18        34.68 
TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-8296 
        9.17        30.90        12.82        15.32         3.45        15.58 
TCGA-BR-8373 TCGA-BR-A4J7 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8528 TCGA-CG-4444 
       14.79        19.36         3.25        13.18         0.10        47.05 
TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-A4YU 
       30.97        12.03        79.07        18.54        15.98        16.44 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-F1-A448 TCGA-FP-7998 TCGA-HU-A4G9 TCGA-HU-A4GD 
       11.24         2.96        21.27        22.29        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       25.81         8.98         2.10        12.95        19.36        12.30 
TCGA-HU-A4HD TCGA-R5-A7ZR TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8P5 TCGA-VQ-A8PK 
       27.42         6.08        35.61        48.79         7.73        17.85 
TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Y 
       23.41        13.35        64.57        65.16        11.93         9.73 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A94O TCGA-VQ-AA6F 
        9.04         2.01        21.04        54.12 

$`3P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94         4.21        32.45         6.21        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        4.67        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M 
       31.56        24.03         6.28         3.16        30.25         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
       25.12         0.36         7.40         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        83.24        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
        5.92        12.66        12.43        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.25         0.10        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.23        12.03        13.18         0.13        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         2.89         1.45         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
       20.38         5.29         3.42         4.80        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       18.81        19.96         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       30.71        18.18        42.87        46.19        15.06         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 
       15.91        10.16         3.42         2.10         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-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-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-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-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-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82         0.66        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-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-D7-6522 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-D7-8576 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-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-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-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-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        6.25        10.19         0.26        23.84         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-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-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73         9.86        45.67        18.21         8.52        61.25 
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-A8DL 
       57.44         8.94        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        35.24        21.73 
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-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       16.31        22.19         2.50        12.79         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A 
        9.27        15.65        26.24        27.35        14.33        36.69 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        61.22        18.74        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 
       36.16         7.36         9.50        52.24        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-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 

  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 
            15.45             12.59 
[1] "0.1 - 79.1 (15.4)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         0        4        5        4         8        14
  3P GAIN WILD-TYPE      11       15       43       28        69        70
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           5         11          8          9        6
  3P GAIN WILD-TYPE        24         86         64         39       45
                   vv
clus                STAGE IVA
  3P GAIN MUTATED           1
  3P GAIN WILD-TYPE         3
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                11
  STAGE IA                 4                15
  STAGE IB                 5                43
  STAGE II                 4                28
  STAGE IIA                8                69
  STAGE IIB               14                70
  STAGE III                5                24
  STAGE IIIA              11                86
  STAGE IIIB               8                64
  STAGE IIIC               9                39
  STAGE IV                 6                45
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3P GAIN MUTATED       6  15  39  16
  3P GAIN WILD-TYPE    47 111 241 108
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1               6                47
  T2                 15               111
  T3                 39               241
  T4                 16               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
  3P GAIN MUTATED    23  25  10  16
  3P GAIN WILD-TYPE 177 157  86  81
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              23               177
  N1              25               157
  N2              10                86
  N3              16                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"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    67   4
  3P GAIN WILD-TYPE 446  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     67    4
  3P GAIN WILD-TYPE  446   35
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              67               446
  1               4                35
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    24  57
  3P GAIN WILD-TYPE 158 370
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     24   57
  3P GAIN WILD-TYPE  158  370
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              24               158
  MALE                57               370
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3P GAIN MUTATED                                       9
  3P GAIN WILD-TYPE                                    62
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                       14
  3P GAIN WILD-TYPE                                                    148
                   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                                           9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         14
  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                                            62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          148
  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  81
  3P GAIN WILD-TYPE   6 522
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   81
  3P GAIN WILD-TYPE    6  522
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                 6
  YES              81               522
[1] 2 2
[1] FALSE
D5V10, continuous
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    44   1   2   4
  3P GAIN WILD-TYPE 303  17  17  21
D5V11, 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"
D5V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED      18                         2
  3P GAIN WILD-TYPE   111                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           0    49
  3P GAIN WILD-TYPE                                         1   336
D5V13, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                                  18               111
  BLACK OR AFRICAN AMERICAN                               2                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  49               336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3  45
  3P GAIN WILD-TYPE   4 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   45
  3P GAIN WILD-TYPE    4  349
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO              45               349
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    96  60
  3Q GAIN WILD-TYPE 258 161
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              156               419 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               60               161 
$`3Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 
       31.27        58.55         7.63        16.24         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       20.09         0.85         2.63        18.64         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43H 
       17.03        14.50        60.39        23.18        25.22         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S 
        4.31        47.93         3.32         3.16         7.13         6.94 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         7.40         3.95        55.50         2.66        35.97 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       16.47        13.22         8.71        13.41        27.12        52.57 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.36        10.45        12.43        13.41         0.10        13.15 
TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-Q9-A6FU TCGA-R6-A6DN 
       15.52        11.54        12.33        10.52         5.16         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC 
        7.59         5.06        53.95        12.69        20.38         3.42 
TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
        9.27        22.82        12.43        18.31         8.12        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-ZR-A9CJ TCGA-B7-5818 
       42.87        15.06        11.24         9.17        19.73        11.70 
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-7723 TCGA-BR-7901 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 
       28.73         3.45         8.05         2.20        15.58        19.50 
TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-A4J4 
       26.33        14.79        25.18        12.79        15.81         0.53 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 
       19.36        20.65        20.42         3.25        13.18         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4444 TCGA-CG-4455 
        0.07         0.10        15.95         7.99        47.05        12.03 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-6521 TCGA-D7-6815 
       12.00        30.97        12.03        79.07        18.54        15.98 
TCGA-D7-8570 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-F1-A448 TCGA-FP-7916 
       24.72        16.44        11.24         2.96        21.27        14.07 
TCGA-FP-7998 TCGA-HJ-7597 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
       22.29        26.47        12.30        24.20        22.75        25.81 
TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4HD TCGA-IN-A6RP 
        8.98         2.10        12.95        19.36        27.42         6.44 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F7 TCGA-R5-A7ZR TCGA-RD-A8MW TCGA-RD-A8N1 
        5.56         1.81        60.56         6.08        37.91       115.69 
TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       35.61        48.79        13.02        18.48        35.24        21.73 
TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PU 
        7.73         2.70        17.85        23.41        13.35        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 
       64.57        65.16        11.93         9.73         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        4.54        21.04        32.94        54.12        21.11         0.79 

$`3Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A5B8 
       32.45         6.21        20.78        20.12         9.30         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       25.41        21.70        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       30.25         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       19.99        21.01        18.35         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        4.90        29.00         7.43         8.71        25.12         0.36 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
        3.02        12.92        13.48        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49U 
       21.37        83.24        46.09         5.92        12.66        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U5 
       13.25         0.10        12.46         0.10        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        0.13        33.11         7.82        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        6.35         9.30        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
       20.02         5.29         4.80        15.35         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7I 
       19.96         1.55        28.11        18.18        46.19        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI 
       10.16         3.42         2.10         2.66        26.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        7.43        18.35        30.90         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       21.11        31.20        32.94         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7957 
       23.93        15.42        28.01        18.15        12.43         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-8285 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       16.31         7.40         6.18        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
       19.17         0.26        15.85         3.72         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22         1.12         9.34        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-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-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.72        14.17        12.82         0.66        13.51         0.46 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        1.15        13.64        11.57         5.13         2.83        13.15 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 
        0.30         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-4306 
        0.10        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       21.99         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-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        12.79        10.55        11.31        12.33 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        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-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-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
       14.47        72.23        11.38         3.48        19.53        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-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-A4H5 
        6.51         6.25        10.19         0.26        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-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
        3.39        18.38         5.36         5.19        13.08         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74        12.59         6.51         7.82        13.51         2.53 
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-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-A8N0 
       11.05         8.61         5.13        16.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.79         0.92         5.46        13.25        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-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50        12.79         1.87         9.27        15.65        26.24 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       14.33        36.69        11.70        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z 
       22.68         1.71        36.16         7.36         9.50        52.24 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         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-AA6B 
       11.24        22.09        18.41        40.08        28.41        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       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 
            13.20             12.56 
[1] "0.1 - 115.7 (13.2)" "0.0 - 122.3 (12.6)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         2        5       12        8        20        22
  3Q GAIN WILD-TYPE       9       14       36       24        57        62
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED          14         21         19         18       10
  3Q GAIN WILD-TYPE        15         76         53         30       41
                   vv
clus                STAGE IVA
  3Q GAIN MUTATED           2
  3Q GAIN WILD-TYPE         2
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 9
  STAGE IA                 5                14
  STAGE IB                12                36
  STAGE II                 8                24
  STAGE IIA               20                57
  STAGE IIB               22                62
  STAGE III               14                15
  STAGE IIIA              21                76
  STAGE IIIB              19                53
  STAGE IIIC              18                30
  STAGE IV                10                41
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3Q GAIN MUTATED      15  30  77  33
  3Q GAIN WILD-TYPE    38  96 203  91
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              15                38
  T2                 30                96
  T3                 77               203
  T4                 33                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q GAIN MUTATED    50  51  22  28
  3Q GAIN WILD-TYPE 150 131  74  69
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              50               150
  N1              51               131
  N2              22                74
  N3              28                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"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   134   8
  3Q GAIN WILD-TYPE 379  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    134    8
  3Q GAIN WILD-TYPE  379   31
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0             134               379
  1               8                31
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    44 119
  3Q GAIN WILD-TYPE 138 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     44  119
  3Q GAIN WILD-TYPE  138  308
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              44               138
  MALE               119               308
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3Q GAIN MUTATED                                      12
  3Q GAIN WILD-TYPE                                    59
                   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                                          12
  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                                            59
  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     1 162
  3Q GAIN WILD-TYPE   5 441
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1  162
  3Q GAIN WILD-TYPE    5  441
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                1                 5
  YES             162               441
[1] 2 2
[1] FALSE
D6V10, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    76   2   5   5
  3Q GAIN WILD-TYPE 271  16  14  20
D6V11, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              76               271
  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"
D6V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED      38                         6
  3Q GAIN WILD-TYPE    91                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           0    95
  3Q GAIN WILD-TYPE                                         1   290
D6V13, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                                  38                91
  BLACK OR AFRICAN AMERICAN                               6                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  95               290
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3  92
  3Q GAIN WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   92
  3Q GAIN WILD-TYPE    4  302
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO              92               302
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    23  13
  4P GAIN WILD-TYPE 331 208
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               36               539 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               208 
$`4P GAIN MUTATED`
TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-L5-A43J TCGA-L5-A4ON TCGA-L5-A8NE 
        2.63        23.41       122.10         4.31        18.35        55.50 
TCGA-L5-A8NV TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HY TCGA-R6-A6XG TCGA-R6-A6Y0 
       52.57        11.54         4.47        12.03        29.59        53.95 
TCGA-R6-A6Y2 TCGA-VR-A8EO TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-BR-8484 TCGA-BR-A4IY 
        9.30        18.81        10.16         2.66        25.18        12.89 
TCGA-CD-8528 TCGA-CG-4443 TCGA-CG-4475 TCGA-CG-5720 TCGA-CG-5722 TCGA-D7-5578 
        0.10        29.98        22.98         0.99         0.99        12.66 
TCGA-D7-5579 TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-HU-A4GH TCGA-IN-7806 TCGA-IN-A7NT 
       11.93        11.24        15.65        11.77        21.21         5.56 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91Q TCGA-VQ-A92D TCGA-VQ-AA6K 
        1.87        13.35        27.35        20.81        64.18        12.43 

$`4P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        6.21        33.27        20.09         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
        6.28         3.16        30.25         0.30         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.68         4.70        32.61        19.99        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       25.12         0.36         7.40         3.95         3.02         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       83.24        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39         0.10        15.52        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-R6-A8W8 
        5.06        14.70         7.04         6.35        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        1.45        12.69         7.00        20.02        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        3.42         4.80        15.35         9.27         4.44        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 
        9.17        15.91         3.42         2.10        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-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-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-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-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-8529 
        0.07         0.07         0.07         0.07         0.07         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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       14.01        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-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         6.02       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-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        7.99        12.36        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        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-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        13.71        11.31        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-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-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-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-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88         8.81        27.42         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
        3.39        18.38         5.36         5.19        13.08         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44         6.74        12.59         6.51         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-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-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-A8PO 
       22.19         2.50        12.79         2.70        17.85         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        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 
            122.1             122.3 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           12.775            12.760 
[1] "0.1 - 122.1 (12.8)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         1        2        3        0         3         8
  4P GAIN WILD-TYPE      10       17       45       32        74        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           1          8          1          1        4
  4P GAIN WILD-TYPE        28         89         71         47       47
                   vv
clus                STAGE IVA
  4P GAIN MUTATED           0
  4P GAIN WILD-TYPE         4
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  1                10
  STAGE IA                 2                17
  STAGE IB                 3                45
  STAGE II                 0                32
  STAGE IIA                3                74
  STAGE IIB                8                76
  STAGE III                1                28
  STAGE IIIA               8                89
  STAGE IIIB               1                71
  STAGE IIIC               1                47
  STAGE IV                 4                47
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4P GAIN MUTATED       5   6  16   6
  4P GAIN WILD-TYPE    48 120 264 118
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               5                48
  T2                  6               120
  T3                 16               264
  T4                  6               118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P GAIN MUTATED    14  12   4   3
  4P GAIN WILD-TYPE 186 170  92  94
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              14               186
  N1              12               170
  N2               4                92
  N3               3                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"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    28   2
  4P GAIN WILD-TYPE 485  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     28    2
  4P GAIN WILD-TYPE  485   37
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              28               485
  1               2                37
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6  30
  4P GAIN WILD-TYPE 176 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6   30
  4P GAIN WILD-TYPE  176  397
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6               176
  MALE                30               397
[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                                                                   3
  4P GAIN WILD-TYPE                                                                78
                   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)               3
  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)                78
  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  36
  4P GAIN WILD-TYPE   6 567
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   36
  4P GAIN WILD-TYPE    6  567
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 6
  YES              36               567
[1] 2 2
[1] FALSE
D7V10, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    17   2   1   0
  4P GAIN WILD-TYPE 330  16  18  25
D7V11, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              17               330
  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"
D7V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED       6                         0
  4P GAIN WILD-TYPE   123                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0    25
  4P GAIN WILD-TYPE                                         1   360
D7V13, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                                   6               123
  BLACK OR AFRICAN AMERICAN                               0                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  25               360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  19
  4P GAIN WILD-TYPE   6 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   19
  4P GAIN WILD-TYPE    6  375
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              19               375
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    17  14
  4Q GAIN WILD-TYPE 337 207
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               31               544 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               207 
$`4Q GAIN MUTATED`
TCGA-IG-A3YA TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A8NE 
       20.78        23.41       122.10         0.30        18.35        55.50 
TCGA-L5-A8NV TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HY TCGA-R6-A6Y0 TCGA-V5-A7RC 
       52.57        15.52        11.54        12.03        53.95         3.42 
TCGA-VR-A8EO TCGA-VR-A8EW TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-BR-8484 TCGA-CG-4475 
       18.81         8.12        10.16         2.66        25.18        22.98 
TCGA-CG-5720 TCGA-CG-5722 TCGA-D7-5578 TCGA-D7-A6EV TCGA-HJ-7597 TCGA-HU-8249 
        0.99         0.99        12.66        11.24        26.47        14.17 
TCGA-IN-7806 TCGA-RD-A8N5 TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A91Q TCGA-VQ-A92D 
       21.21        57.44         1.87        27.35        20.81        64.18 
TCGA-VQ-A94T 
       11.24 

$`4Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
        6.21        33.27        20.09         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        6.28         3.16        30.25         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.68         4.70        32.61        19.99        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       25.12         0.36         7.40         3.95         3.02         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       83.24        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59        22.39         0.10        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        5.06        14.70         7.04        29.59         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         4.80        15.35         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       19.96        22.82        12.43         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 
        9.17        15.91         3.42         2.10        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-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-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-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-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-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
       12.00        30.97         6.97        36.00         1.02         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-D7-5579 
        4.01        69.04        21.07         7.99        12.36        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-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       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-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-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-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-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-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-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-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-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-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       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-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79         2.70        17.85         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        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 
              0.3               0.0 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            122.1             122.3 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           18.350            12.675 
[1] "0.3 - 122.1 (18.4)" "0.0 - 122.3 (12.7)"
[1] "hr=" "1.2"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         1        0        3        0         4         6
  4Q GAIN WILD-TYPE      10       19       45       32        73        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           2          6          3          0        3
  4Q GAIN WILD-TYPE        27         91         69         48       48
                   vv
clus                STAGE IVA
  4Q GAIN MUTATED           0
  4Q GAIN WILD-TYPE         4
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                10
  STAGE IA                 0                19
  STAGE IB                 3                45
  STAGE II                 0                32
  STAGE IIA                4                73
  STAGE IIB                6                78
  STAGE III                2                27
  STAGE IIIA               6                91
  STAGE IIIB               3                69
  STAGE IIIC               0                48
  STAGE IV                 3                48
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4Q GAIN MUTATED       3   7  15   4
  4Q GAIN WILD-TYPE    50 119 265 120
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               3                50
  T2                  7               119
  T3                 15               265
  T4                  4               120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q GAIN MUTATED    11  10   6   2
  4Q GAIN WILD-TYPE 189 172  90  95
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              11               189
  N1              10               172
  N2               6                90
  N3               2                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"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    25   1
  4Q GAIN WILD-TYPE 488  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     25    1
  4Q GAIN WILD-TYPE  488   38
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              25               488
  1               1                38
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5  26
  4Q GAIN WILD-TYPE 177 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5   26
  4Q GAIN WILD-TYPE  177  401
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               5               177
  MALE                26               401
[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                                                                   1
  4Q GAIN WILD-TYPE                                                                80
                   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)               1
  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)                80
  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  31
  4Q GAIN WILD-TYPE   6 572
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   31
  4Q GAIN WILD-TYPE    6  572
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                 6
  YES              31               572
[1] 2 2
[1] FALSE
D8V10, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    14   0   1   0
  4Q GAIN WILD-TYPE 333  18  18  25
D8V11, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              14               333
  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"
D8V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED       5                         1
  4Q GAIN WILD-TYPE   124                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0    20
  4Q GAIN WILD-TYPE                                         1   365
D8V13, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                                   5               124
  BLACK OR AFRICAN AMERICAN                               1                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  20               365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0  16
  4Q GAIN WILD-TYPE   7 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   16
  4Q GAIN WILD-TYPE    7  378
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              16               378
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   102  58
  5P GAIN WILD-TYPE 252 163
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              160               415 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               58               163 
$`5P GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC 
       14.30         5.92        32.45        33.27         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD 
       18.64         0.79        23.41        14.50        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43J 
        3.68        42.77        31.56        25.22         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        8.94        32.61        19.99        47.93         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y 
        3.16         4.90        29.00         7.13         6.94         0.36 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NV TCGA-L7-A6VZ 
       55.50        35.97        12.92        13.55        52.57        10.36 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 
       13.41         0.10        13.25        12.46        12.59        12.59 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW 
        0.10        12.33        13.22         4.47        12.33        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.23        12.03        13.18         5.16         5.06        14.70 
TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EX 
       53.95         7.00        20.38         3.42        19.96        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JD 
       30.71        42.87        15.06        11.24        15.91         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-BR-4187 TCGA-BR-7704 TCGA-BR-7715 
        2.10         2.66        19.73         4.64        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 
       28.01        18.15         3.45        11.44         0.69         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 
       12.95         2.66        15.58         0.26        17.52        26.33 
TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4PD 
       14.79         9.21        20.22        11.54         8.22        20.65 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48C 
       13.18         0.07         0.07         0.10         3.42        11.61 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
        7.99        54.08        14.01        47.05        12.03        21.99 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5722 
       18.97         7.07        12.00        22.98        36.00         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6527 TCGA-D7-6528 
       12.03        15.02         4.01        11.93        10.26        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 
       10.55        11.31        24.72        14.66        11.31         2.96 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8238 
       15.65         0.62        19.53        17.06         0.23         1.51 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.59        14.17        24.30         3.25        22.75        25.81 
TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        2.10        12.30        27.42         6.51         5.56         1.81 
TCGA-KB-A6F5 TCGA-KB-A93G TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8N5 TCGA-RD-A8N6 
        5.56        20.15        45.67        18.21        57.44         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       35.61         5.46        13.25        18.48        35.24        21.73 
TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A 
       17.85        36.69         9.50        11.24        40.08        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       54.12        16.14        21.11        12.43 

$`5P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21         7.69         6.21        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 
       20.78         3.88         9.30         0.53        17.03        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB 
        9.96        14.86         4.67        12.16       122.10        60.39 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        25.41        21.70        23.18        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ 
        3.16        30.25        24.00         3.68         4.70        21.01 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
       18.35         1.38        58.59         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI 
       25.12         7.40         3.95         3.02         2.66        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L 
       13.41        27.12        83.24        46.09         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.66        12.43        13.15        15.35         0.10         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 
       12.49        12.76        22.39        15.52        11.54        25.25 
TCGA-LN-A7HV TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       10.52         0.13        33.11         7.82         8.02         7.59 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        29.59         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        1.45        12.69        20.02         5.29         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        18.81        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7D TCGA-X8-AAAR 
       18.31         8.12        18.18        46.19         9.17        10.16 
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-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-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-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        0.56         5.52        18.08        26.47         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        12.10        10.62         0.76         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       11.84        24.20        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        0.10         6.51         6.25        10.19         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        23.84         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-AB1V 
       13.08         1.41         6.44         6.74        12.59         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        60.56        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        9.86         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-A8NB TCGA-SW-A7EA 
       40.64       115.69       116.38        71.38        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.79         0.92        48.79        13.02        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-A8PM TCGA-VQ-A8PO 
       22.19         2.50        12.79         2.70         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-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-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 
       18.41        28.41        29.98        17.13        26.04        10.62 
TCGA-ZQ-A9CR 
        0.79 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.07              0.00 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            68.02            122.30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           13.065            12.690 
[1] "0.1 - 68.0 (13.1)"  "0.0 - 122.3 (12.7)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         1        4       14        9        24        21
  5P GAIN WILD-TYPE      10       15       34       23        53        63
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED          11         25         14         16       16
  5P GAIN WILD-TYPE        18         72         58         32       35
                   vv
clus                STAGE IVA
  5P GAIN MUTATED           1
  5P GAIN WILD-TYPE         3
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                10
  STAGE IA                 4                15
  STAGE IB                14                34
  STAGE II                 9                23
  STAGE IIA               24                53
  STAGE IIB               21                63
  STAGE III               11                18
  STAGE IIIA              25                72
  STAGE IIIB              14                58
  STAGE IIIC              16                32
  STAGE IV                16                35
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5P GAIN MUTATED       9  38  90  23
  5P GAIN WILD-TYPE    44  88 190 101
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1               9                44
  T2                 38                88
  T3                 90               190
  T4                 23               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
  5P GAIN MUTATED    54  51  26  27
  5P GAIN WILD-TYPE 146 131  70  70
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              54               146
  N1              51               131
  N2              26                70
  N3              27                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"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   136  13
  5P GAIN WILD-TYPE 377  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    136   13
  5P GAIN WILD-TYPE  377   26
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             136               377
  1              13                26
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    48 119
  5P GAIN WILD-TYPE 134 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     48  119
  5P GAIN WILD-TYPE  134  308
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              48               134
  MALE               119               308
[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                                                                  28
  5P GAIN WILD-TYPE                                                                53
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5P GAIN MUTATED                                                 16
  5P GAIN WILD-TYPE                                               62
                   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)              28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               16
  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)                53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 62
  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     2 165
  5P GAIN WILD-TYPE   4 438
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2  165
  5P GAIN WILD-TYPE    4  438
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                2                 4
  YES             165               438
[1] 2 2
[1] FALSE
D9V10, continuous
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    80   4   5   5
  5P GAIN WILD-TYPE 267  14  14  20
D9V11, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              80               267
  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"
D9V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED      36                         3
  5P GAIN WILD-TYPE    93                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           0   104
  5P GAIN WILD-TYPE                                         1   281
D9V13, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                                  36                93
  BLACK OR AFRICAN AMERICAN                               3                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 104               281
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  97
  5P GAIN WILD-TYPE   6 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   97
  5P GAIN WILD-TYPE    6  297
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              97               297
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    42  17
  5Q GAIN WILD-TYPE 312 204
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               59               516 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17               204 
$`5Q GAIN MUTATED`
TCGA-IG-A3I8 TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI 
       33.27        25.22         0.30         8.94        32.61        19.99 
TCGA-L5-A4OO TCGA-L5-A88S TCGA-L7-A6VZ TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4MR 
        3.32         6.94        10.36        12.46        12.59        13.22 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-RE-A7BO 
       12.00        12.23        12.03         5.06        14.70         7.00 
TCGA-V5-A7RC TCGA-VR-AA7B TCGA-VR-AA7I TCGA-BR-7715 TCGA-BR-8284 TCGA-BR-8296 
        3.42        11.24        15.91        15.42         8.05        15.58 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-A4PD TCGA-CD-8524 TCGA-CD-A486 TCGA-CG-4436 
       17.52        26.33        20.65         0.07         3.42         7.99 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-6528 
       12.03        18.97        12.00        15.02         4.01        15.22 
TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6F2 TCGA-FP-7829 TCGA-FP-8099 TCGA-HU-8238 
       24.72        14.66        15.65        19.53        17.06         1.51 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-IN-A7NR TCGA-IN-A7NT 
       12.59        14.17         2.10        12.30         6.51         5.56 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93G TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-VQ-A8E0 
        1.81         5.56        20.15        57.44        35.61        18.48 
TCGA-VQ-A91X TCGA-VQ-A94T TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6K 
        9.50        11.24        54.12        16.14        12.43 

$`5Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        6.21        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       12.16       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OE 
       24.03         6.28         3.16        30.25         4.31        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        3.68         4.70        21.01        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.43         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33         4.47        12.33        25.25        10.52 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW 
       15.78         2.89         1.45        12.69        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        10.16         3.42         2.10         2.66        19.73 
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-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
        4.01        14.01        29.98        47.05        19.07        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        79.07        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        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-D7-6527 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-D7-8572 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-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-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-8243 TCGA-HU-8244 
        5.52         0.23        18.08        26.47         5.92        14.27 
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-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         0.26        12.95        19.36        23.84 
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-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-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-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 
       37.91        40.64       115.69       116.38        71.38         8.94 
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-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-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-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        64.18        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-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        17.13        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 
            12.46             12.79 
[1] "0.1 - 57.4 (12.5)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         1        0        8        4        12         4
  5Q GAIN WILD-TYPE      10       19       40       28        65        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           3          7          6          8        4
  5Q GAIN WILD-TYPE        26         90         66         40       47
                   vv
clus                STAGE IVA
  5Q GAIN MUTATED           0
  5Q GAIN WILD-TYPE         4
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                10
  STAGE IA                 0                19
  STAGE IB                 8                40
  STAGE II                 4                28
  STAGE IIA               12                65
  STAGE IIB                4                80
  STAGE III                3                26
  STAGE IIIA               7                90
  STAGE IIIB               6                66
  STAGE IIIC               8                40
  STAGE IV                 4                47
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5Q GAIN MUTATED       2  15  35   7
  5Q GAIN WILD-TYPE    51 111 245 117
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               2                51
  T2                 15               111
  T3                 35               245
  T4                  7               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
  5Q GAIN MUTATED    24  13   8  13
  5Q GAIN WILD-TYPE 176 169  88  84
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              24               176
  N1              13               169
  N2               8                88
  N3              13                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"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    51   3
  5Q GAIN WILD-TYPE 462  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     51    3
  5Q GAIN WILD-TYPE  462   36
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              51               462
  1               3                36
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    16  46
  5Q GAIN WILD-TYPE 166 381
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     16   46
  5Q GAIN WILD-TYPE  166  381
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              16               166
  MALE                46               381
[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                                                       11
  5Q GAIN WILD-TYPE                                                    151
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                                  11
  5Q GAIN WILD-TYPE                                                                70
                   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                                                           2
  5Q GAIN WILD-TYPE                                                         6
                   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)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  5Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                70
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 71
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         17
  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"
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  61
  5Q GAIN WILD-TYPE   5 542
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   61
  5Q GAIN WILD-TYPE    5  542
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                1                 5
  YES              61               542
[1] 2 2
[1] FALSE
D10V10, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    37   1   1   1
  5Q GAIN WILD-TYPE 310  17  18  24
D10V11, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              37               310
  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"
D10V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED      14                         2
  5Q GAIN WILD-TYPE   115                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    36
  5Q GAIN WILD-TYPE                                         1   349
D10V13, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                                  14               115
  BLACK OR AFRICAN AMERICAN                               2                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  36               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  38
  5Q GAIN WILD-TYPE   7 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   38
  5Q GAIN WILD-TYPE    7  356
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              38               356
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    57  47
  6P GAIN WILD-TYPE 297 174
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              104               471 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               47               174 
$`6P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A4QS 
       25.78        31.27        14.30        13.94        16.24         3.88 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A4OM 
        4.67        14.50       122.10        68.02        30.25        47.93 
TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       58.59         6.94         2.60         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L7-A6VZ 
        2.66        12.92         5.49        21.37        27.12        10.36 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4MQ TCGA-LN-A7HW TCGA-LN-A7HX 
       10.45        13.15         0.10        12.33        12.00        12.23 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-B7-A5TJ 
       14.70         7.04        15.78        15.91         2.10        11.01 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        6.61         6.97         9.17         9.21        35.24        15.42 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 
       18.15        28.73        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-IN-A6RS TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BT 
       18.38         1.41        12.59        45.67        18.21         8.61 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       37.91       115.69         8.94        13.25        13.02        18.48 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91X 
       22.19         2.70        17.85        18.74         1.71         9.50 
TCGA-VQ-A91Y TCGA-VQ-A94O 
        9.73        21.04 

$`6P GAIN WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       58.55         7.63         5.92         8.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I 
        0.79        23.41        12.82         9.96        14.86        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       44.75        60.39         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16         0.30         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        4.70        32.61        19.99        21.01        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NG 
        7.43         8.71        25.12         0.36         7.40        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR 
       13.48        16.47        13.55        13.22         7.76         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M 
       13.41        83.24        52.57        46.09         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41         0.10        15.35         0.10        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        11.54        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       25.25        10.52        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
        5.16         7.82         8.02         7.59         5.06        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        42.87        46.19        15.06        11.24         9.17 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
       10.16         3.42         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         9.44         4.64         7.43        18.35 
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-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       23.93        28.01        15.32        12.43         3.45         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-8291 TCGA-BR-8295 
        9.60        20.55         8.05         0.56        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-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-8483 
       11.80        19.17         0.26        15.85         3.72         5.39 
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-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-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65         1.15        13.64        11.57         5.13         2.83 
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-A489 TCGA-CD-A48A 
        0.10         0.13         0.13         0.10        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-4441 
       27.02        15.95         1.02         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       29.98        47.05        19.07         0.00         9.01         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-D7-6519 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-D7-6815 TCGA-D7-6817 
       18.54        18.61        17.85        13.35        15.98        12.79 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        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-7829 TCGA-FP-7916 
       14.47        72.23        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-A8CX 
       22.29        17.06        59.54         5.03        13.58         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-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-A4H5 
       10.19         0.26         2.10        12.95        19.36        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-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR 
        5.36         5.19        13.08         6.44         6.74         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-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13        16.67       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79         5.46        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-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        12.79         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-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-A91Q TCGA-VQ-A91S 
       36.69        11.70        11.93        61.22        20.81        22.68 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       36.16         7.36        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-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-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 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              0.1               0.0 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            122.1             122.3 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           12.935            12.760 
[1] "0.1 - 122.1 (12.9)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         4        4       12        6        12        15
  6P GAIN WILD-TYPE       7       15       36       26        65        69
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           6         18         12          5       11
  6P GAIN WILD-TYPE        23         79         60         43       40
                   vv
clus                STAGE IVA
  6P GAIN MUTATED           3
  6P GAIN WILD-TYPE         1
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  4                 7
  STAGE IA                 4                15
  STAGE IB                12                36
  STAGE II                 6                26
  STAGE IIA               12                65
  STAGE IIB               15                69
  STAGE III                6                23
  STAGE IIIA              18                79
  STAGE IIIB              12                60
  STAGE IIIC               5                43
  STAGE IV                11                40
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6P GAIN MUTATED      12  28  51  18
  6P GAIN WILD-TYPE    41  98 229 106
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1              12                41
  T2                 28                98
  T3                 51               229
  T4                 18               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
  6P GAIN MUTATED    39  33  19  17
  6P GAIN WILD-TYPE 161 149  77  80
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              39               161
  N1              33               149
  N2              19                77
  N3              17                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"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    93   9
  6P GAIN WILD-TYPE 420  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     93    9
  6P GAIN WILD-TYPE  420   30
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              93               420
  1               9                30
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    33  80
  6P GAIN WILD-TYPE 149 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     33   80
  6P GAIN WILD-TYPE  149  347
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              33               149
  MALE                80               347
[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                                                       31
  6P GAIN WILD-TYPE                                                    131
                   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)                         31
  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)                          131
  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     3 110
  6P GAIN WILD-TYPE   3 493
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3  110
  6P GAIN WILD-TYPE    3  493
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                3                 3
  YES             110               493
[1] 2 2
[1] FALSE
D11V10, continuous
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    56   3   5   6
  6P GAIN WILD-TYPE 291  15  14  19
D11V11, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              56               291
  R1               3                15
  R2               5                14
  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"
D11V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED      21                         4
  6P GAIN WILD-TYPE   108                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           1    72
  6P GAIN WILD-TYPE                                         0   313
D11V13, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                                  21               108
  BLACK OR AFRICAN AMERICAN                               4                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  72               313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     1  72
  6P GAIN WILD-TYPE   6 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   72
  6P GAIN WILD-TYPE    6  322
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              72               322
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    46  42
  6Q GAIN WILD-TYPE 308 179
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               88               487 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               42               179 
$`6Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A4QS 
       31.27        14.30         7.63        13.94        16.24         3.88 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A88S 
       14.50       122.10        60.39        68.02        30.25         6.94 
TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NQ 
        2.60         3.02        55.50         2.66        12.92        21.37 
TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4MQ 
       27.12        10.36        10.45        13.15         0.10        12.33 
TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-VR-AA7I 
        4.47        12.23        14.70         7.04        15.78        15.91 
TCGA-Z6-A8JE TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-7197 TCGA-BR-7704 
        2.10        11.01         6.61         6.97         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 
       15.42        18.15        28.73        11.44        12.95         2.66 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
       14.04        14.79        25.18         9.21        20.22        11.54 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CD-A486 TCGA-CG-4436 
       15.68        10.68         0.72         3.25         3.42         7.99 
TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4477 TCGA-D7-6527 TCGA-D7-6528 
       54.08        21.99        18.97        30.97        10.26        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-FP-7735 
       10.55        11.31        12.33        14.27         7.99         3.48 
TCGA-FP-A4BF TCGA-HU-A4GT TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
        5.52         6.51         9.67         3.45         3.39        18.38 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A8N6 TCGA-VQ-A8DV 
        1.41        12.59        45.67         8.61         8.94        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91N 
       13.02        18.48        22.19         2.70        17.85        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A94R 
       22.68         1.71         9.50        42.54 

$`6Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       25.78        58.55         5.92         8.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       12.16        44.75         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16         0.30         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
       29.00         7.13         7.43         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         3.95        35.97        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09         5.92        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
        0.10        15.35         0.10        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       11.54        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59         5.06        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        4.44        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD 
       46.19        15.06        11.24         9.17        10.16         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        9.44         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-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       28.01        15.32        12.43         3.45         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-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         8.05         0.56        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-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8487 
       19.17         0.26        15.85         3.72         5.39         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-8687 TCGA-BR-A44T 
        0.49        15.81        16.44         9.86         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-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-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-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-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-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         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-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-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       17.19        15.98        12.79        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-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-A4SO TCGA-F1-6874 
        4.34         7.40         7.13         0.62        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX 
       17.06        59.54         5.03        13.58         0.56         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-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-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-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         8.88         8.81        27.42        21.21 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81         5.36         5.19        13.08         6.44         6.74 
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 
              0.1               0.0 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            122.1             122.3 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            12.46             12.79 
[1] "0.1 - 122.1 (12.5)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         5        3       10        5        10        10
  6Q GAIN WILD-TYPE       6       16       38       27        67        74
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           6         15          9          3       13
  6Q GAIN WILD-TYPE        23         82         63         45       38
                   vv
clus                STAGE IVA
  6Q GAIN MUTATED           3
  6Q GAIN WILD-TYPE         1
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  5                 6
  STAGE IA                 3                16
  STAGE IB                10                38
  STAGE II                 5                27
  STAGE IIA               10                67
  STAGE IIB               10                74
  STAGE III                6                23
  STAGE IIIA              15                82
  STAGE IIIB               9                63
  STAGE IIIC               3                45
  STAGE IV                13                38
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6Q GAIN MUTATED      12  22  40  18
  6Q GAIN WILD-TYPE    41 104 240 106
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1              12                41
  T2                 22               104
  T3                 40               240
  T4                 18               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q GAIN MUTATED    34  30  12  15
  6Q GAIN WILD-TYPE 166 152  84  82
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              34               166
  N1              30               152
  N2              12                84
  N3              15                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"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    76  11
  6Q GAIN WILD-TYPE 437  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     76   11
  6Q GAIN WILD-TYPE  437   28
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              76               437
  1              11                28
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    25  71
  6Q GAIN WILD-TYPE 157 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     25   71
  6Q GAIN WILD-TYPE  157  356
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              25               157
  MALE                71               356
[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                                                       28
  6Q GAIN WILD-TYPE                                                    134
                   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)                         28
  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)                          134
  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  93
  6Q GAIN WILD-TYPE   3 510
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   93
  6Q GAIN WILD-TYPE    3  510
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                3                 3
  YES              93               510
[1] 2 2
[1] FALSE
D12V10, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    46   2   4   6
  6Q GAIN WILD-TYPE 301  16  15  19
D12V11, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              46               301
  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"
D12V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED      17                         4
  6Q GAIN WILD-TYPE   112                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           1    60
  6Q GAIN WILD-TYPE                                         0   325
D12V13, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                                  17               112
  BLACK OR AFRICAN AMERICAN                               4                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  60               325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1  59
  6Q GAIN WILD-TYPE   6 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   59
  6Q GAIN WILD-TYPE    6  335
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              59               335
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   173 108
  7P GAIN WILD-TYPE 181 113
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              281               294 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              108               113 
$`7P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78         5.92        13.94         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
        7.69        20.09         2.63        20.12        18.64         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A939 
       17.03         0.79        23.41        14.50        60.39        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       23.18        25.22         3.16        30.25         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO 
       24.00         3.68         4.70        32.61        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88S 
        1.38         3.16        58.59         4.90         7.13         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         0.36         3.95         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR 
       12.92        16.47        13.55        13.22         5.49         8.71 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       27.12        52.57        46.09        10.36         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41         0.10        15.35         0.10        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       12.59        12.49        12.76        12.59         0.10        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-Q9-A6FW 
       13.22        12.33        25.25        12.00         0.13         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35        53.95         9.30         1.45        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         3.42        15.35         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN 
       46.19        11.24        15.91        10.16         2.10         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-6456 
       19.73        11.70        11.01         6.97         4.64        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-7901 TCGA-BR-7958 TCGA-BR-7959 
       35.24        15.42        18.15         3.45        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 
       14.43         0.69         8.05         0.56        12.95         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 
       15.58         7.40        13.08         0.95         3.32        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 
        0.26         5.39        20.22         1.12        16.44         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
        8.22        10.68        22.26         1.48        12.89         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
        0.53        19.36        13.51        20.65        20.42        13.64 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
        3.25        13.18         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-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6F0 TCGA-D7-A6F2 
       21.14        20.91        16.44        15.16         2.96        15.65 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 
       17.06         0.23        26.47        14.17        24.30        12.30 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
        3.25        22.75        25.81         8.98         0.10        10.19 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD 
        2.10        12.95        19.36        23.84        12.30        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-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GQ TCGA-IC-A6RF 
       31.27        14.30        58.55         7.63         4.21         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 
       33.27         0.85        20.78         3.88         9.30        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D 
       68.02         3.68        41.52        42.77        25.41        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
       24.03         6.28         8.94        19.99        21.01        47.93 
TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
        7.17        29.00         7.43         8.71        25.12         7.40 
TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       55.50        13.48         7.76        21.37        13.41        83.24 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A8 
       10.45        12.66        13.15        12.46        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       11.54         4.47        10.52        12.23        12.03        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-A7RE 
       33.11         5.16        15.78         2.89        20.02         4.80 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       18.81        22.82        12.43        18.18        42.87        15.06 
TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
        9.17         3.42        26.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.61         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-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       39.12        26.10        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       31.20        32.94        12.82        24.76        23.93        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8060 
       15.32        28.73        12.43         9.07        17.49        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 
       12.26         9.60        20.55         2.66        16.31         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
       19.50         0.26        22.19        17.52        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       14.04        11.80        19.17        15.85         3.72        25.18 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T 
        7.53         0.49        11.54        15.81        15.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       13.87         7.53         6.08        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL 
       14.17        12.82         0.66         0.46         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83        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-8531 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         0.13         9.34        11.31         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 
        3.02         1.02         8.05        54.08        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 
       19.07        12.03         0.00         9.01        18.97        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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 
       15.02        65.10         4.01        69.04        12.36        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8572 
       18.61        17.85        13.35        12.79        11.31        16.80 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27         5.92        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.31        11.44         9.76         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        16.24        21.27        11.38 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         5.52        18.08 
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-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH 
       10.62         0.76         5.59        11.84        24.20        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H6 
       21.37        29.98         6.51         6.25         0.26         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
        8.88         8.81        21.21         5.36        13.08         6.74 
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-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-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       22.19         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91S 
       13.35        26.24        27.35        64.57        61.22        22.68 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        52.24         9.04        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
       64.18         2.66        18.41        28.41        17.13        26.04 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              0.1               0.0 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            122.3             122.1 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           12.920            12.575 
[1] "0.1 - 122.3 (12.9)" "0.0 - 122.1 (12.6)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         8        7       24       15        35        42
  7P GAIN WILD-TYPE       3       12       24       17        42        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED          19         42         32         25       21
  7P GAIN WILD-TYPE        10         55         40         23       30
                   vv
clus                STAGE IVA
  7P GAIN MUTATED           3
  7P GAIN WILD-TYPE         1
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  8                 3
  STAGE IA                 7                12
  STAGE IB                24                24
  STAGE II                15                17
  STAGE IIA               35                42
  STAGE IIB               42                42
  STAGE III               19                10
  STAGE IIIA              42                55
  STAGE IIIB              32                40
  STAGE IIIC              25                23
  STAGE IV                21                30
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7P GAIN MUTATED      31  54 142  51
  7P GAIN WILD-TYPE    22  72 138  73
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              31                22
  T2                 54                72
  T3                142               138
  T4                 51                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"
                   vv
clus                 N0  N1  N2  N3
  7P GAIN MUTATED    96  88  45  46
  7P GAIN WILD-TYPE 104  94  51  51
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              96               104
  N1              88                94
  N2              45                51
  N3              46                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"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   241  17
  7P GAIN WILD-TYPE 272  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    241   17
  7P GAIN WILD-TYPE  272   22
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             241               272
  1              17                22
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    71 228
  7P GAIN WILD-TYPE 111 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     71  228
  7P GAIN WILD-TYPE  111  199
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              71               111
  MALE               228               199
[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                                                       69
  7P GAIN WILD-TYPE                                                     93
                   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)                         69
  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)                           93
  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     3 296
  7P GAIN WILD-TYPE   3 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3  296
  7P GAIN WILD-TYPE    3  307
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                3                 3
  YES             296               307
[1] 2 2
[1] FALSE
D13V10, continuous
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   160   7   6   9
  7P GAIN WILD-TYPE 187  11  13  16
D13V11, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             160               187
  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"
D13V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED      62                         9
  7P GAIN WILD-TYPE    67                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           1   188
  7P GAIN WILD-TYPE                                         0   197
D13V13, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                                  62                67
  BLACK OR AFRICAN AMERICAN                               9                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 188               197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     6 183
  7P GAIN WILD-TYPE   1 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6  183
  7P GAIN WILD-TYPE    1  211
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 1
  NOT HISPANIC OR LATINO             183               211
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   144  90
  7Q GAIN WILD-TYPE 210 131
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              234               341 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               90               131 
$`7Q GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
       25.78         8.94        16.24        32.45         7.69        20.09 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FB 
       20.12        18.64        17.03        23.41        14.50        60.39 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        31.56        25.22         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31        24.00         3.68         4.70        32.61 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A88S 
       47.93         3.32         3.16        58.59         4.90         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         0.36         3.95         3.02         2.66        35.97 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.22         5.49        27.12        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        5.92        13.41         0.10        15.35         0.10        13.25 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.49        12.76         0.10        15.52        11.54        12.33 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.33        25.25        12.00         0.13         7.82         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC 
       14.70         7.04        29.59         6.35         9.30         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       12.69         7.00        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
        9.27        19.96        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       18.18        46.19        11.24        10.16         2.10        19.73 
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-CD-5799 TCGA-CD-5801 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A48A 
        3.25        13.18         0.16         0.13         0.10        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        6.58        12.20        20.02        27.02        15.95         7.99 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 
        4.01        14.01         7.07        12.00        22.98        36.00 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 
       12.03        28.96        79.07        21.07        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       19.13        18.84        18.54        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       15.98        24.72        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 
       20.91        16.44         2.96        15.65        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HJ-7597 
        3.48        14.07        22.29        17.06         0.23        26.47 
TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ 
       14.17        24.30        12.30        25.81         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-IN-8462 
       10.19         2.10        12.95        19.36        23.84        18.81 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NR TCGA-KB-A6F5 
        3.39         5.19         1.41         6.44         6.51         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       60.56        20.15         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 
       61.25         6.08         8.61       122.30        57.44         8.94 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PB 
       48.79        13.25        35.24        21.73        34.45        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       46.26         2.50        17.85        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.70        11.93        20.81         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 
        9.50         2.01         4.54        21.04        11.24        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       32.94        29.98        54.12        16.14        10.62         0.79 

$`7Q GAIN WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30         0.53         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC 
        3.68        41.52        42.77        25.41        24.03         6.28 
TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.94        19.99        21.01        18.35         7.17         1.38 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.13         7.43         8.71        25.12         7.40 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
       55.50        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
       21.37         8.71        13.41        83.24        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 
       12.43        13.15         0.10        12.46        12.59        12.59 
TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       22.39        13.22         4.47        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 
       13.18        33.11         5.16         7.59         5.06        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EO 
       15.78         2.89        20.02         4.80         4.44        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
       22.82        12.43         1.55        42.87        15.06         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK 
       15.91         3.42         2.66        26.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        9.44         6.61         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-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       39.12        26.10        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       31.20        32.94        12.82        24.76        23.93        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 
       15.32        28.73        12.43         3.45         9.07        17.49 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 
       11.44         0.69        12.26         9.60        20.55         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-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 
       26.33         4.31        14.04        11.80        19.17        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        25.18         9.21        12.79        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-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68         8.22        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-A4J2 
       22.26         1.48        13.41        13.51         8.98        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       12.82         0.66         0.46         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83        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-8531 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
        0.10         0.13         3.42         9.34        11.31        11.61 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        0.10        12.62         3.02         1.02         8.05        54.08 
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-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        9.01        18.97        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 
       69.04         7.99        12.36        20.55        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       13.35        12.79        10.55        11.31        12.33        16.80 
TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       18.21        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-A747 
       13.71        11.24        11.31        11.44         9.76         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-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       21.27        11.38        19.53        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.56         5.52        18.08         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       12.59        11.41        12.10        10.62         0.76         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H6 
       29.98         6.51         6.25         0.26        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI 
        8.88         8.81        27.42        21.21         3.45        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        5.36        13.08         6.74        12.59         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        7.82        13.51         2.53        37.64         3.72        19.73 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        4.60         9.24        11.05         5.13        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       115.69       116.38        71.38        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       19.04         5.79         0.92         5.46        13.02        18.48 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PD TCGA-VQ-A8PE 
       27.88        32.48         7.73        28.96        16.31        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91N 
       13.35        26.24        27.35        64.57        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
       22.68         9.73        52.24         9.04        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 
        5.72        64.18         2.66        42.54        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       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 
            122.3             122.1 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            13.33             12.43 
[1] "0.1 - 122.3 (13.3)" "0.0 - 122.1 (12.4)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         7        7       21       14        29        30
  7Q GAIN WILD-TYPE       4       12       27       18        48        54
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED          13         34         28         24       17
  7Q GAIN WILD-TYPE        16         63         44         24       34
                   vv
clus                STAGE IVA
  7Q GAIN MUTATED           3
  7Q GAIN WILD-TYPE         1
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  7                 4
  STAGE IA                 7                12
  STAGE IB                21                27
  STAGE II                14                18
  STAGE IIA               29                48
  STAGE IIB               30                54
  STAGE III               13                16
  STAGE IIIA              34                63
  STAGE IIIB              28                44
  STAGE IIIC              24                24
  STAGE IV                17                34
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7Q GAIN MUTATED      27  48 119  39
  7Q GAIN WILD-TYPE    26  78 161  85
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              27                26
  T2                 48                78
  T3                119               161
  T4                 39                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"
                   vv
clus                 N0  N1  N2  N3
  7Q GAIN MUTATED    82  68  38  42
  7Q GAIN WILD-TYPE 118 114  58  55
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              82               118
  N1              68               114
  N2              38                58
  N3              42                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"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   200  14
  7Q GAIN WILD-TYPE 313  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    200   14
  7Q GAIN WILD-TYPE  313   25
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             200               313
  1              14                25
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    61 190
  7Q GAIN WILD-TYPE 121 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     61  190
  7Q GAIN WILD-TYPE  121  237
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              61               121
  MALE               190               237
[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                                                       60
  7Q GAIN WILD-TYPE                                                    102
                   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)                         60
  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)                          102
  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     2 249
  7Q GAIN WILD-TYPE   4 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  249
  7Q GAIN WILD-TYPE    4  354
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                2                 4
  YES             249               354
[1] 2 2
[1] FALSE
D14V10, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   136   4   5  11
  7Q GAIN WILD-TYPE 211  14  14  14
D14V11, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             136               211
  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"
D14V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED      50                         8
  7Q GAIN WILD-TYPE    79                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           1   160
  7Q GAIN WILD-TYPE                                         0   225
D14V13, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                                  50                79
  BLACK OR AFRICAN AMERICAN                               8                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 160               225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     6 152
  7Q GAIN WILD-TYPE   1 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6  152
  7Q GAIN WILD-TYPE    1  242
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 1
  NOT HISPANIC OR LATINO             152               242
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   141  86
  8P GAIN WILD-TYPE 213 135
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              227               348 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               86               135 
$`8P GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       14.30         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 
       20.09        20.78        17.03        12.82         4.67       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       68.02         3.68        31.56        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.30         4.31        19.99        47.93        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y 
        3.16         4.90         7.13         7.43         2.60         0.36 
TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS 
       35.97        13.55        13.22         7.76        21.37        13.41 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       10.36         5.92        13.41        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DQ 
        0.10        12.59         0.10        12.03        13.18         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE 
        5.06         7.04        15.78        12.69         7.00         4.80 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D 
       15.35        19.96        22.82         8.12        18.18        46.19 
TCGA-VR-AA7B TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TJ 
       11.24         3.42         2.10        19.73        26.70        11.01 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-6452 
        9.47         6.61         6.97         4.64        30.90        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6707 TCGA-BR-6802 
       15.95        13.87        13.68         9.17        19.89        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7957 
       31.20        32.94        35.24        23.93        15.42         9.07 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8297 TCGA-BR-8368 
       11.44        12.26         9.60         8.05         7.40         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 
       14.04         3.32        19.17         0.26        15.85         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-A452 
        9.21        20.22         9.34        13.45         7.53         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
       22.26         1.48        13.41        12.82        19.36         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8530 TCGA-CD-8536 
       20.42        11.57        13.15         0.07         0.16         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 
        3.42         9.34         6.58        12.62        20.02        15.95 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4466 
       14.01        47.05        12.03        21.99         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5726 
        7.07        12.00        36.00         0.99        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       79.07        65.10        21.07        12.66        11.93        19.13 
TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       18.84        17.85        17.19        12.79        10.55        12.33 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV 
       14.66        20.91         5.92        15.16        14.76        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-EQ-A4SO 
       11.31        11.44         2.96         8.38         4.34        16.24 
TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       21.27        19.53         5.52         0.23        18.08        26.47 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       14.27        12.59        11.41        24.30        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.10         0.26         2.10        19.36        23.84        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RS 
        8.88         8.81         3.45         3.39         5.19        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UJ 
        6.51         5.56        60.56        20.15        37.64        19.73 
TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 
        9.86         8.52        61.25         6.08        16.67       115.69 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       13.02        27.88        28.96        34.29        16.31        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PU 
       12.79         2.70         9.27        23.41        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A927 
       64.57        36.69        11.93        36.16         7.36         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U TCGA-ZA-A8F6 
        5.72        21.04        42.54        22.09        10.62 

$`8P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
        7.69         6.21         0.85         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        3.88         9.30         0.53         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG 
       14.86        14.50        12.16        44.75        60.39        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-KH-A6WC 
       42.77        25.41        21.70        23.18        25.22         6.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        8.94        24.00         3.68         4.70        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T 
        3.32         7.17        58.59        29.00         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT 
       12.92        13.48        16.47         5.49         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        46.09        10.45        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.15        12.46        12.59        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO 
       12.33        25.25        10.52        12.00        12.23         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG 
       33.11         5.16         7.82         8.02        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BV 
        6.35        53.95         9.30         2.89         1.45        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.38         5.29         3.42         9.27         4.44        18.81 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
       12.43         1.55        18.31        28.11        30.71        42.87 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-B7-5818 
       15.06         9.17        15.91        10.16         2.66        11.70 
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 
       19.56         9.44         7.43        18.35         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
        6.61        17.29        19.33        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-7196 
       25.61        18.05        12.16         8.98        21.11        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        24.76        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.69        20.55         0.56        12.95         2.66        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-8371 TCGA-BR-8373 
       22.19        17.52         0.95        26.33        11.80        14.79 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8592 
        3.72        25.18         1.12        12.79        15.81         6.28 
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-A4IV 
        8.22        10.68        12.56        13.87         6.08        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       13.51        20.65         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        3.25        13.18         0.30         0.07         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-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13        11.31        12.43        11.61        12.20         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-4477 
        4.01        29.98        19.07         9.01        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
        6.97         1.02         0.99         6.02       105.07        12.03 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 
        4.01        69.04         7.99        12.36        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
       18.61        13.35        10.26        15.22        15.98        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.27        16.44        13.78        13.71         9.76        15.65 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         0.62         7.99        14.47        72.23 
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-HU-8238 TCGA-HU-8243 TCGA-HU-8249 
        5.03        13.58         0.56         1.51         5.92        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GJ 
       12.10        10.62         0.76         5.59        11.77        21.37 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD 
        6.51         6.25        10.19        12.95         9.67        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO 
       21.21        18.81        18.38         5.36        13.08         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.44         6.74         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A804 TCGA-R5-A805 
        5.56         3.72        45.67        18.21         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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        35.24        21.73        34.45        32.48         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       46.26         2.50        17.85         1.87        15.65        13.35 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       14.33        65.16        11.70        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       22.68         1.71         9.50         9.73        52.24         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T 
        2.01        55.43         4.54        64.18         2.66        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-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       54.12        26.04        16.14        21.11        12.43         0.79 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.00              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            122.1             122.3 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           12.820            12.625 
[1] "0.0 - 122.1 (12.8)" "0.1 - 122.3 (12.6)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         3        9       23       13        27        38
  8P GAIN WILD-TYPE       8       10       25       19        50        46
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED          14         37         22         21       18
  8P GAIN WILD-TYPE        15         60         50         27       33
                   vv
clus                STAGE IVA
  8P GAIN MUTATED           2
  8P GAIN WILD-TYPE         2
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  3                 8
  STAGE IA                 9                10
  STAGE IB                23                25
  STAGE II                13                19
  STAGE IIA               27                50
  STAGE IIB               38                46
  STAGE III               14                15
  STAGE IIIA              37                60
  STAGE IIIB              22                50
  STAGE IIIC              21                27
  STAGE IV                18                33
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8P GAIN MUTATED      21  52 109  49
  8P GAIN WILD-TYPE    32  74 171  75
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              21                32
  T2                 52                74
  T3                109               171
  T4                 49                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
  8P GAIN MUTATED    81  67  36  43
  8P GAIN WILD-TYPE 119 115  60  54
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              81               119
  N1              67               115
  N2              36                60
  N3              43                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"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   206  15
  8P GAIN WILD-TYPE 307  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    206   15
  8P GAIN WILD-TYPE  307   24
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             206               307
  1              15                24
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    85 158
  8P GAIN WILD-TYPE  97 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     85  158
  8P GAIN WILD-TYPE   97  269
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              85                97
  MALE               158               269
[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                                                       62
  8P GAIN WILD-TYPE                                                    100
                   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                                                 30
  8P GAIN WILD-TYPE                                               48
                   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                                          7
  8P GAIN WILD-TYPE                                        6
D15V8, multiclass
                                                                   clus
vv                                                                  8P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         62
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        7
                                                                   clus
vv                                                                  8P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            40
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          100
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          8
  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"
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     4 239
  8P GAIN WILD-TYPE   2 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4  239
  8P GAIN WILD-TYPE    2  364
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                4                 2
  YES             239               364
[1] 2 2
[1] FALSE
D15V10, continuous
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED   138  11   5  15
  8P GAIN WILD-TYPE 209   7  14  10
D15V11, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0             138               209
  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"
D15V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED      47                         6
  8P GAIN WILD-TYPE    82                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           0   156
  8P GAIN WILD-TYPE                                         1   229
D15V13, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                                  47                82
  BLACK OR AFRICAN AMERICAN                               6                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 156               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"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3 153
  8P GAIN WILD-TYPE   4 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3  153
  8P GAIN WILD-TYPE    4  241
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             153               241
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   190 116
  8Q GAIN WILD-TYPE 164 105
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              306               269 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              116               105 
$`8Q GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
       14.30        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        33.27        20.09        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        3.88        17.03        12.82         4.67        14.50       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C 
       68.02         3.68        23.18        31.56        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30         4.31        19.99        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         1.38         3.16         4.90         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.60         0.36        35.97        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        27.12        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       10.36         5.92        13.41         0.10        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
       13.25         0.10        12.59        12.59         0.10        11.54 
TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.33        12.23        12.03        13.18         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04        53.95        15.78        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
       20.38         4.80        15.35         9.27         4.44        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       22.82        12.43         8.12        30.71        18.18        46.19 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       11.24         9.17        15.91         3.42         2.10        19.73 
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-6456 TCGA-BR-6457 
       30.90        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6565 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        9.17        19.89        12.16        30.90        31.20        32.94 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7957 
        9.21        35.24        23.93        15.42        28.01         9.07 
TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       12.76        11.44         0.69        12.26         9.60         8.05 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8367 TCGA-BR-8368 
       15.58         7.40         6.18        13.08        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 
       14.04         3.32        19.17         0.26        15.85         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 
        9.21        20.22        12.79         9.34        13.45         7.53 
TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       16.44         8.22        13.87         7.53        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL 
       13.41         0.72        12.82        19.36         0.46        11.57 
TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 
       13.15         0.07         0.07         0.07         0.16         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MJ 
        0.13         0.10         3.42         9.34         6.58        12.62 
TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       20.02        15.95         7.99         8.05        54.08        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4466 
       29.98        47.05        12.03        21.99         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5725 
        7.07        12.00        22.98        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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       14.66        20.91        16.44         5.92        15.16        14.76 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44         2.96        15.65         8.38 
TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
        4.34         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        3.48        19.53         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-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-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N1 
        8.52        61.25         6.08        11.05        16.67       115.69 
TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       71.38        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
        5.46        13.25        13.02        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-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E 
       13.35        26.24        27.35        64.57        36.69        11.93 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
       36.16         7.36        52.24         6.58         5.72        21.04 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6K TCGA-ZA-A8F6 
       42.54        22.09        18.41        40.08        12.43        10.62 

$`8Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-IC-A6RF 
       25.78        31.27        58.55         7.63         5.92         6.21 
TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.85        18.64         9.30         0.53         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG 
        9.96        14.86        12.16        44.75        60.39        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43M 
       42.77        25.41        21.70        25.22         6.28         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP 
       24.00         3.68         4.70        32.61        21.01         7.17 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       58.59        29.00         6.94         8.71        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       16.47        83.24        52.57        10.45        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 
       13.15        12.46        12.49        12.76        22.39        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 
        0.13        33.11         5.16         7.82         8.02        14.70 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-V5-A7RB 
       29.59         6.35         9.30         2.89         1.45         5.29 
TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 
        3.42        18.81         1.55        18.31        28.11        42.87 
TCGA-VR-AA4G TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN 
       15.06        10.16         2.66        11.70        19.56         9.44 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6458 
        7.43        18.35         6.18         9.57         6.61        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 
       39.12        26.10        32.78        25.61        18.05         8.98 
TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       21.11        12.82        24.76        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8081 
       12.43         3.45        18.71        17.49        14.43        20.55 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8361 
        0.56        12.95         2.66        16.31         2.20        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8371 TCGA-BR-8373 
        0.26        22.19        17.52         0.95        11.80        14.79 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8592 TCGA-BR-8677 
        3.72        25.18         1.12        15.81         6.28         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       11.54        15.81         9.86        15.68        10.68        12.56 
TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        6.08        13.51        12.89         8.98        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 
        5.13         2.83         3.25        13.18         0.30         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A489 
        0.07         0.10         0.13         0.10         0.10        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4301 TCGA-CG-4304 
       12.43        11.61        12.20         0.10         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 
        1.02         4.01        19.07         9.01        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5734 
        1.02         0.99         6.02       105.07        12.03         7.99 
TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6527 TCGA-D7-6528 
       12.36        20.55        18.54        18.61        10.26        15.22 
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-A4YY TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A74A TCGA-D7-A74B 
       14.27        13.78        13.71         9.76         7.40         7.13 
TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       14.47        11.38        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        5.03        13.58         1.51        14.17        12.10        10.62 
TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 
        5.59        11.77        21.37        10.19        12.95         9.67 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NU 
       21.21        18.81        18.38         5.36        13.08         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-R5-A804 
        7.82        13.51         2.53         5.56         3.72         4.60 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        9.24         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8E0 TCGA-VQ-A8E2 
      116.38        57.44         8.94        35.61        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PF 
       21.73        34.45        32.48         7.73        46.26         2.50 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       17.85         1.87        15.65        14.33        65.16        11.70 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X 
       61.22        18.74        20.81        22.68         1.71         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A92D 
        9.73         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 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        21.11         0.79 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.00              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            122.1             122.3 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           12.725            12.820 
[1] "0.0 - 122.1 (12.7)" "0.1 - 122.3 (12.8)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         4       13       28       16        35        52
  8Q GAIN WILD-TYPE       7        6       20       16        42        32
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED          19         54         31         30       23
  8Q GAIN WILD-TYPE        10         43         41         18       28
                   vv
clus                STAGE IVA
  8Q GAIN MUTATED           2
  8Q GAIN WILD-TYPE         2
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  4                 7
  STAGE IA                13                 6
  STAGE IB                28                20
  STAGE II                16                16
  STAGE IIA               35                42
  STAGE IIB               52                32
  STAGE III               19                10
  STAGE IIIA              54                43
  STAGE IIIB              31                41
  STAGE IIIC              30                18
  STAGE IV                23                28
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8Q GAIN MUTATED      28  68 152  64
  8Q GAIN WILD-TYPE    25  58 128  60
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              28                25
  T2                 68                58
  T3                152               128
  T4                 64                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"
                   vv
clus                 N0  N1  N2  N3
  8Q GAIN MUTATED   103 101  47  56
  8Q GAIN WILD-TYPE  97  81  49  41
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             103                97
  N1             101                81
  N2              47                49
  N3              56                41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   278  18
  8Q GAIN WILD-TYPE 235  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    278   18
  8Q GAIN WILD-TYPE  235   21
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             278               235
  1              18                21
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   105 223
  8Q GAIN WILD-TYPE  77 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    105  223
  8Q GAIN WILD-TYPE   77  204
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             105                77
  MALE               223               204
[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                                                       84
  8Q GAIN WILD-TYPE                                                     78
                   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                                                         15
  8Q GAIN WILD-TYPE                                                        6
                   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                                          8
  8Q GAIN WILD-TYPE                                        5
D16V8, multiclass
                                                                   clus
vv                                                                  8Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          35
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         84
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        8
                                                                   clus
vv                                                                  8Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            36
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           78
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          6
  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"
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     5 323
  8Q GAIN WILD-TYPE   1 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5  323
  8Q GAIN WILD-TYPE    1  280
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                5                 1
  YES             323               280
[1] 2 2
[1] FALSE
D16V10, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   184  15   7  17
  8Q GAIN WILD-TYPE 163   3  12   8
D16V11, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             184               163
  R1              15                 3
  R2               7                12
  RX              17                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED      68                         9
  8Q GAIN WILD-TYPE    61                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           0   205
  8Q GAIN WILD-TYPE                                         1   180
D16V13, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                                  68                61
  BLACK OR AFRICAN AMERICAN                               9                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 205               180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     4 212
  8Q GAIN WILD-TYPE   3 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4  212
  8Q GAIN WILD-TYPE    3  182
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             212               182
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    49  19
  9P GAIN WILD-TYPE 305 202
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               68               507 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               202 
$`9P GAIN MUTATED`
TCGA-2H-A9GL TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A93C TCGA-L5-A4OO TCGA-L5-A4OU 
        5.92        12.82       122.10        23.18         3.32        29.00 
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49V TCGA-R6-A6L4 
        0.36        27.12        10.36        13.41         0.10        14.70 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-B7-A5TK TCGA-BR-6456 TCGA-BR-6707 
       15.06         9.17         2.66         9.47        17.29        19.89 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8588 
       23.93        15.42         9.60         2.66         2.20        12.79 
TCGA-BR-8682 TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8535 
       16.44         0.53         0.46         2.83        13.18         0.13 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4477 TCGA-D7-6528 
       12.20         7.99        47.05        21.99        30.97        15.22 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-EQ-5647 
       10.55        12.33        18.21        14.76        11.44         0.62 
TCGA-F1-A448 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 
       21.27         0.23        18.08        14.17         0.76        12.30 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-8663 
       22.75         8.98         2.10        12.95        12.30         3.39 
TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-KB-A93G TCGA-R5-A7ZI TCGA-RD-A8MV TCGA-RD-A8N1 
        6.44        60.56        20.15        61.25       122.30       115.69 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PP TCGA-VQ-A91S TCGA-VQ-A91Z 
       35.61         5.46        46.26        23.41        22.68        52.24 
TCGA-VQ-A922 TCGA-VQ-A928 
        9.04         5.72 

$`9P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        3.16        30.25         0.30         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.68         4.70        32.61        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       46.09         5.92        10.45        12.66        12.43         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       10.52        12.00        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       33.11         5.16         7.82         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        2.89         1.45        12.69         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       18.81        19.96        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        30.71        18.18        42.87        46.19 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       11.24        15.91        10.16         3.42         2.10        19.73 
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-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-8291 
       12.26        20.55         8.05         0.56        12.95        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-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-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-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81         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-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       12.82         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64        11.57         5.13         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-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-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58         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-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-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-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       10.26        15.98        12.79        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        15.16        13.78        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         7.99        16.24        14.47        72.23 
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-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        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-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       10.62        24.30         5.59        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-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.25        10.19         0.26        19.36        23.84         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-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR 
       18.38         5.36         5.19        13.08         1.41         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-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53         5.56        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-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-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-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-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-A923 TCGA-VQ-A924 
       36.16         7.36         9.50         9.73         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58        64.18        21.04         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-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 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              0.1               0.0 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           122.30            116.38 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           12.885            12.690 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (12.7)"
[1] "hr=" "1.6"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         2        2        8        3        10         8
  9P GAIN WILD-TYPE       9       17       40       29        67        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           1         11          9          8        7
  9P GAIN WILD-TYPE        28         86         63         40       44
                   vv
clus                STAGE IVA
  9P GAIN MUTATED           0
  9P GAIN WILD-TYPE         4
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  2                 9
  STAGE IA                 2                17
  STAGE IB                 8                40
  STAGE II                 3                29
  STAGE IIA               10                67
  STAGE IIB                8                76
  STAGE III                1                28
  STAGE IIIA              11                86
  STAGE IIIB               9                63
  STAGE IIIC               8                40
  STAGE IV                 7                44
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9P GAIN MUTATED       8  15  32  16
  9P GAIN WILD-TYPE    45 111 248 108
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               8                45
  T2                 15               111
  T3                 32               248
  T4                 16               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
  9P GAIN MUTATED    26  18  12  15
  9P GAIN WILD-TYPE 174 164  84  82
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              26               174
  N1              18               164
  N2              12                84
  N3              15                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"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    65   4
  9P GAIN WILD-TYPE 448  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     65    4
  9P GAIN WILD-TYPE  448   35
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              65               448
  1               4                35
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    22  51
  9P GAIN WILD-TYPE 160 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     22   51
  9P GAIN WILD-TYPE  160  376
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              22               160
  MALE                51               376
[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                                                       16
  9P GAIN WILD-TYPE                                                    146
                   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                                                 13
  9P GAIN WILD-TYPE                                               65
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9P GAIN MUTATED                                                          7
  9P GAIN WILD-TYPE                                                       14
                   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)                         16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        7
  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)                          146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                74
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 65
  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"
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  71
  9P GAIN WILD-TYPE   4 532
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   71
  9P GAIN WILD-TYPE    4  532
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2                 4
  YES              71               532
[1] 2 2
[1] FALSE
D17V10, continuous
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    47   3   2   2
  9P GAIN WILD-TYPE 300  15  17  23
D17V11, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              47               300
  R1               3                15
  R2               2                17
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED      20                         1
  9P GAIN WILD-TYPE   109                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           0    40
  9P GAIN WILD-TYPE                                         1   345
D17V13, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                                  20               109
  BLACK OR AFRICAN AMERICAN                               1                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  40               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  46
  9P GAIN WILD-TYPE   5 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   46
  9P GAIN WILD-TYPE    5  348
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              46               348
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    64  33
  9Q GAIN WILD-TYPE 290 188
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               97               478 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               33               188 
$`9Q GAIN MUTATED`
TCGA-2H-A9GL TCGA-IC-A6RE TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FB 
        5.92         7.69         0.53        12.82       122.10        60.39 
TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L5-A8NT 
       23.18         3.16         3.32        29.00         0.36        27.12 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A9 
       10.36         5.92        13.41         0.10         0.10        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-R6-A6L4 TCGA-S8-A6BV TCGA-VR-A8ER TCGA-VR-AA4G 
       12.33         4.47        14.70        20.02        12.43        15.06 
TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-B7-A5TK TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6707 
        9.17         2.66         9.47        18.35        17.29        19.89 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8080 
       35.24        23.93        15.42        18.15        18.71         9.60 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-A4J4 
        2.66         2.20         6.18        12.79        16.44         0.53 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8535 
        0.46        20.65        20.42         2.83        13.18         0.13 
TCGA-CG-4436 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4477 TCGA-D7-5578 TCGA-D7-6526 
        7.99        47.05        21.99        30.97        12.66        17.19 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A6F2 
       15.22        10.55        14.27        14.76        11.44        15.65 
TCGA-D7-A747 TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-A8CX TCGA-HF-A5NB 
        8.38         0.62        21.27         3.48         0.23        18.08 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP 
        1.51        14.17         0.76        12.30        22.75         8.98 
TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-KB-A6F7 
       12.30         3.45         3.39         1.41         6.44        60.56 
TCGA-KB-A93G TCGA-R5-A7ZI TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT 
       20.15        61.25       122.30       115.69        35.61        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A91N TCGA-VQ-A91S 
        5.46        46.26        23.41        27.35        18.74        22.68 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A94T 
       36.16         9.50        52.24         9.04         5.72        11.24 
TCGA-VQ-AA6K 
       12.43 

$`9Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        3.88         9.30        17.03         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
        3.68        41.52        42.77        25.41        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       25.22        24.03         6.28        30.25         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       58.59         4.90         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        46.09        10.45        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
        0.10        13.15        15.35        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
        9.27         4.44        18.81        19.96        22.82         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       46.19        11.24        15.91        10.16         3.42         2.10 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       19.73        26.70        11.70        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-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-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-7716 TCGA-BR-7722 
       32.94        12.82         9.21        24.76        28.01        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       28.73        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        0.56        12.95        16.31        15.58         7.40        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-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        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-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17        12.82         0.66        19.36        13.51 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64        11.57         5.13         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-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-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-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
       18.97         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-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-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        11.93        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-D7-6820 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-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        15.16        13.78        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.31         9.76         2.96         4.34         7.40         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 
        7.99        16.24        14.47        72.23        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-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        0.56         5.52        26.47         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       11.41        12.10        10.62        24.30         5.59        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-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-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       27.42        21.21        18.81        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       13.08         6.74        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG 
        7.82        13.51         2.53         5.56        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73         9.86        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-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       37.91        40.64       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87        19.04         5.79         0.92        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-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       12.79         2.70        17.85         1.87         9.27        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-A91Q TCGA-VQ-A91U TCGA-VQ-A91W 
       11.70        11.93        61.22        20.81         1.71         7.36 
TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.73         2.01        55.43         4.54         6.58        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        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-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        10.62         0.79 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              0.1               0.0 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           122.30            116.38 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            12.79             12.76 
[1] "0.1 - 122.3 (12.8)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.2"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         3        3       10        4        13        12
  9Q GAIN WILD-TYPE       8       16       38       28        64        72
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           4         20         11          8       10
  9Q GAIN WILD-TYPE        25         77         61         40       41
                   vv
clus                STAGE IVA
  9Q GAIN MUTATED           0
  9Q GAIN WILD-TYPE         4
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  3                 8
  STAGE IA                 3                16
  STAGE IB                10                38
  STAGE II                 4                28
  STAGE IIA               13                64
  STAGE IIB               12                72
  STAGE III                4                25
  STAGE IIIA              20                77
  STAGE IIIB              11                61
  STAGE IIIC               8                40
  STAGE IV                10                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9Q GAIN MUTATED      11  20  47  22
  9Q GAIN WILD-TYPE    42 106 233 102
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1              11                42
  T2                 20               106
  T3                 47               233
  T4                 22               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
  9Q GAIN MUTATED    35  31  17  18
  9Q GAIN WILD-TYPE 165 151  79  79
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              35               165
  N1              31               151
  N2              17                79
  N3              18                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"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    91   6
  9Q GAIN WILD-TYPE 422  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     91    6
  9Q GAIN WILD-TYPE  422   33
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              91               422
  1               6                33
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    26  78
  9Q GAIN WILD-TYPE 156 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     26   78
  9Q GAIN WILD-TYPE  156  349
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              26               156
  MALE                78               349
[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                                                       23
  9Q GAIN WILD-TYPE                                                    139
                   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)                         23
  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)                          139
  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     2 102
  9Q GAIN WILD-TYPE   4 501
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2  102
  9Q GAIN WILD-TYPE    4  501
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                2                 4
  YES             102               501
[1] 2 2
[1] FALSE
D18V10, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    64   4   2   3
  9Q GAIN WILD-TYPE 283  14  17  22
D18V11, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              64               283
  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"
D18V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED      27                         2
  9Q GAIN WILD-TYPE   102                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           0    58
  9Q GAIN WILD-TYPE                                         1   327
D18V13, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                                  27               102
  BLACK OR AFRICAN AMERICAN                               2                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  58               327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  67
  9Q GAIN WILD-TYPE   5 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   67
  9Q GAIN WILD-TYPE    5  327
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              67               327
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    79  48
  10P GAIN WILD-TYPE 275 173
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               127                448 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                48                173 
$`10P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       58.55        13.94        16.24        32.45         7.69         6.21 
TCGA-IG-A3YC TCGA-JY-A6F8 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH 
       20.12       122.10        25.22         3.16         3.68        32.61 
TCGA-L5-A4OR TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.16         2.60         3.02        55.50        12.92        16.47 
TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A4A1 
        8.71        10.36        10.45         0.10        13.15        12.59 
TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XQ 
        0.10        12.33        12.23         8.02         5.06         6.35 
TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-AASW TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8Q7 
       15.78        20.38         9.27         1.55        18.31        42.87 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 
       46.19        10.16         2.10        17.29        13.68         9.17 
TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
       21.11         9.21        15.42        28.01        18.15        28.73 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        0.69         9.60        12.95         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A4J1 
        7.40         5.39         9.21        16.44         9.86         0.72 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5801 
       19.36        13.51        20.65         1.15        13.64        13.18 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.07         0.07         0.16         9.34        12.43        11.61 
TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4477 
       20.02         4.01        47.05        21.99        12.00        30.97 
TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 
        4.01        19.13        20.55        18.84        17.19        10.55 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       21.14        16.44        11.31        15.65         7.40         0.62 
TCGA-F1-6875 TCGA-FP-7735 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8610 
       72.23         3.48         1.51         5.92        11.41         0.76 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU 
       12.30        24.20        22.75        25.81        11.77         6.25 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 
       12.95        23.84         9.67        27.42         3.45         3.39 
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-A94U 
       64.57        14.33        11.93         1.71         4.54        22.09 
TCGA-VQ-AA6J 
       21.11 

$`10P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30         7.63         5.92         8.94 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       42.77        25.41        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        6.28        30.25         0.30         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        4.70        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.43         6.94         8.71        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        3.95         2.66        35.97        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49        21.37        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09         5.92        12.66        12.43        13.41 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       15.35         0.10        13.25         0.10        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59        22.39        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
       13.22         4.47        25.25        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
       13.18         0.13        33.11         5.16         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
       14.70         7.04        29.59        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
        1.45        12.69         7.00        20.02         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80        15.35         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G 
       12.43         8.12        28.11        30.71        18.18        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24         9.17        15.91         3.42         2.66        19.73 
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-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-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-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 
       12.82        24.76        35.24        23.93        15.32        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-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       11.44        12.26        20.55         8.05         0.56        16.31 
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-8484 
       19.17        14.79         0.26        15.85         3.72        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 
        6.28         7.53         0.49        11.54        15.81        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-A4J9 TCGA-BR-A4PE 
       14.17         0.53        12.82         0.66         0.46        20.42 
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-5803 TCGA-CD-8525 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-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-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-4441 
       15.95         1.02         7.99         8.05        54.08        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-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-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       12.66        11.93        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       13.71        11.24        11.44         9.76         2.96         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-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47        14.27        12.59        14.17        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.30         5.59        11.84         3.25        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       19.36        12.30         8.88         8.81        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-MX-A5UG 
       13.51         2.53         5.56        60.56        20.15         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-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        9.24         5.13        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-A8E0 
        5.79         0.92        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       35.24        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31        22.19         2.50         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       65.16        36.69        11.70        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       22.68        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-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        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-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       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 
            12.330             12.805 
[1] "0.1 - 122.3 (12.3)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1"  
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         4        8        8        5        14        21
  10P GAIN WILD-TYPE       7       11       40       27        63        63
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           6         25         14          7       11
  10P GAIN WILD-TYPE        23         72         58         41       40
                    vv
clus                 STAGE IVA
  10P GAIN MUTATED           2
  10P GAIN WILD-TYPE         2
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   4                  7
  STAGE IA                  8                 11
  STAGE IB                  8                 40
  STAGE II                  5                 27
  STAGE IIA                14                 63
  STAGE IIB                21                 63
  STAGE III                 6                 23
  STAGE IIIA               25                 72
  STAGE IIIB               14                 58
  STAGE IIIC                7                 41
  STAGE IV                 11                 40
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10P GAIN MUTATED      18  22  62  25
  10P GAIN WILD-TYPE    35 104 218  99
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1               18                 35
  T2                  22                104
  T3                  62                218
  T4                  25                 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
  10P GAIN MUTATED    46  39  22  18
  10P GAIN WILD-TYPE 154 143  74  79
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               46                154
  N1               39                143
  N2               22                 74
  N3               18                 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"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   109  10
  10P GAIN WILD-TYPE 404  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    109   10
  10P GAIN WILD-TYPE  404   29
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0              109                404
  1               10                 29
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    38  95
  10P GAIN WILD-TYPE 144 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     38   95
  10P GAIN WILD-TYPE  144  332
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               38                144
  MALE                 95                332
[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                                                       32
  10P GAIN WILD-TYPE                                                    130
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                                  17
  10P GAIN WILD-TYPE                                                                64
                    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)                          32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               17
  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)                           130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 64
  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     2 131
  10P GAIN WILD-TYPE   4 472
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2  131
  10P GAIN WILD-TYPE    4  472
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                  4
  YES              131                472
[1] 2 2
[1] FALSE
D19V10, continuous
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    77   2   6   4
  10P GAIN WILD-TYPE 270  16  13  21
D19V11, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               77                270
  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"
D19V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED      34                         4
  10P GAIN WILD-TYPE    95                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           1    79
  10P GAIN WILD-TYPE                                         0   306
D19V13, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                                   34                 95
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   79                306
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  91
  10P GAIN WILD-TYPE   7 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   91
  10P GAIN WILD-TYPE    7  303
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               91                303
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    54  39
  10Q GAIN WILD-TYPE 300 182
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                93                482 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                39                182 
$`10Q GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A5B8 
       58.55        13.94        16.24         7.69         6.21         0.79 
TCGA-JY-A6F8 TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OR 
      122.10        25.22         4.31         3.68        32.61         3.16 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L 
        3.02        55.50        12.92        16.47        10.36        10.45 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A1 TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W5 
       13.15         0.10        12.59         5.06         6.35        15.78 
TCGA-S8-A6BW TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-BR-6456 
       20.38        22.82        42.87        10.16        19.73        17.29 
TCGA-BR-6564 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8077 
       26.10         9.21        15.42        28.01        28.73         0.69 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8682 TCGA-BR-A4J1 
       12.95         2.66        15.58         7.40        16.44         0.72 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 
       19.36        20.65         1.15        13.18         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4300 TCGA-CG-4444 TCGA-CG-4460 
        0.16         0.13         9.34        20.02        47.05        21.99 
TCGA-CG-4472 TCGA-CG-4477 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 
       12.00        30.97        20.55        18.84        17.19        10.55 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A74A 
       18.21        21.14        16.44        11.24        11.31         7.40 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8610 
        0.62        72.23         3.48         1.51        11.41         0.76 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8663 
       12.30        24.20        22.75         9.67         3.45         3.39 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV TCGA-VQ-A8E3 
       18.21         6.08        11.05         8.61       122.30        21.73 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q 
       46.26        12.79        64.57        14.33        11.93        20.81 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94U 
        4.54         5.72        22.09 

$`10Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30         7.63         5.92         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       24.03         6.28         3.16        30.25         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       24.00         4.70        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI 
        0.36         7.40         3.95         2.66        35.97        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        46.09         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
       12.66        12.43        13.41         0.10        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04        29.59        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        2.89         1.45        12.69         7.00        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 
       15.91         3.42         2.10         2.66        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       12.82        24.76        35.24        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-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-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-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-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       11.93        19.13        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 
       24.72        16.80        19.50        17.19        14.66        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
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-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         7.99        16.24        14.47        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56         5.52         0.23        18.08        26.47 
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-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       24.30         5.59        11.84         3.25        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.25 
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-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 
            12.920             12.725 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (12.7)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         4        7        6        5         6        16
  10Q GAIN WILD-TYPE       7       12       42       27        71        68
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           4         20         10          4        9
  10Q GAIN WILD-TYPE        25         77         62         44       42
                    vv
clus                 STAGE IVA
  10Q GAIN MUTATED           2
  10Q GAIN WILD-TYPE         2
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   4                  7
  STAGE IA                  7                 12
  STAGE IB                  6                 42
  STAGE II                  5                 27
  STAGE IIA                 6                 71
  STAGE IIB                16                 68
  STAGE III                 4                 25
  STAGE IIIA               20                 77
  STAGE IIIB               10                 62
  STAGE IIIC                4                 44
  STAGE IV                  9                 42
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10Q GAIN MUTATED      15  14  49  16
  10Q GAIN WILD-TYPE    38 112 231 108
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1               15                 38
  T2                  14                112
  T3                  49                231
  T4                  16                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
  10Q GAIN MUTATED    35  26  19  13
  10Q GAIN WILD-TYPE 165 156  77  84
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               35                165
  N1               26                156
  N2               19                 77
  N3               13                 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"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    79   7
  10Q GAIN WILD-TYPE 434  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     79    7
  10Q GAIN WILD-TYPE  434   32
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               79                434
  1                7                 32
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    28  69
  10Q GAIN WILD-TYPE 154 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     28   69
  10Q GAIN WILD-TYPE  154  358
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               28                154
  MALE                 69                358
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10Q GAIN MUTATED                                      10
  10Q GAIN WILD-TYPE                                    61
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                       23
  10Q GAIN WILD-TYPE                                                    139
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                                  11
  10Q GAIN WILD-TYPE                                                                70
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  10Q GAIN MUTATED                                                 17
  10Q GAIN WILD-TYPE                                               61
                    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                                           10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                17
  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                                             61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 70
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  61
  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  95
  10Q GAIN WILD-TYPE   4 508
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   95
  10Q GAIN WILD-TYPE    4  508
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                  4
  YES               95                508
[1] 2 2
[1] FALSE
D20V10, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    57   1   4   3
  10Q GAIN WILD-TYPE 290  17  15  22
D20V11, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               57                290
  R1                1                 17
  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"
D20V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED      20                         3
  10Q GAIN WILD-TYPE   109                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           1    62
  10Q GAIN WILD-TYPE                                         0   323
D20V13, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                                   20                109
  BLACK OR AFRICAN AMERICAN                                3                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   62                323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0  66
  10Q GAIN WILD-TYPE   7 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   66
  10Q GAIN WILD-TYPE    7  328
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               66                328
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    48  42
  11P GAIN WILD-TYPE 306 179
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                90                485 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                42                179 
$`11P GAIN MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE 
        8.94        16.24        14.50       122.10        60.39         3.68 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A8NF 
        8.94        24.00        47.93         1.38        29.00         2.66 
TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49V 
        5.49        13.41        52.57        46.09         5.92         0.10 
TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.46        12.33        13.22         4.47         7.82         7.59 
TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY 
        7.04         7.00         3.42        22.82         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-AA7I TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-BR-6455 TCGA-BR-7704 
       18.18        15.91        19.73        11.01        13.87        35.24 
TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8296 TCGA-BR-8678 TCGA-BR-8686 
        3.45        17.49        11.44        15.58        11.54        15.68 
TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A487 
       22.26        12.89        13.51         0.07         0.10         9.34 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-5722 TCGA-D7-6526 TCGA-D7-8576 
       12.20        20.02        54.08         0.99        17.19        14.66 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8243 
        2.96         7.99        14.07        17.06         0.23         5.92 
TCGA-HU-A4G2 TCGA-HU-A4HD TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A7NT TCGA-IN-A7NU 
       24.30        27.42         5.36         1.41         5.56         1.81 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 
        5.56        37.64        61.25         8.61        16.67       115.69 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        8.94        35.61         5.46        13.02        18.48        35.24 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91S TCGA-VQ-A91U 
       22.19         2.70        64.57        14.33        22.68         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
        9.50         9.73        40.08        32.94        29.98        54.12 

$`11P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       13.94         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96        14.86         4.67        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        0.30         4.31         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        18.35         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L7-A6VZ 
        7.76        21.37         8.71        27.12        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       15.35        13.25         0.10        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.13        33.11         5.16         8.02         5.06        14.70 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       29.59         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        1.45        12.69        20.02        20.38         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         4.44        18.81        19.96        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        1.55        18.31        28.11        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       11.24         9.17        10.16         3.42         2.10         2.66 
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-A91N TCGA-VQ-A91Q TCGA-VQ-A91V 
       11.70        11.93        61.22        18.74        20.81        36.16 
TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36        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-AA6D TCGA-VQ-AA6G 
       11.24        22.09        18.41        28.41        17.13        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 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.07               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             122.1              122.3 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            13.315             12.660 
[1] "0.1 - 122.1 (13.3)" "0.0 - 122.3 (12.7)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         2        3        6        2        11        13
  11P GAIN WILD-TYPE       9       16       42       30        66        71
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           6         14         14         10        8
  11P GAIN WILD-TYPE        23         83         58         38       43
                    vv
clus                 STAGE IVA
  11P GAIN MUTATED           2
  11P GAIN WILD-TYPE         2
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   2                  9
  STAGE IA                  3                 16
  STAGE IB                  6                 42
  STAGE II                  2                 30
  STAGE IIA                11                 66
  STAGE IIB                13                 71
  STAGE III                 6                 23
  STAGE IIIA               14                 83
  STAGE IIIB               14                 58
  STAGE IIIC               10                 38
  STAGE IV                  8                 43
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11P GAIN MUTATED       8  11  53  20
  11P GAIN WILD-TYPE    45 115 227 104
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                8                 45
  T2                  11                115
  T3                  53                227
  T4                  20                104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P GAIN MUTATED    26  27  24  14
  11P GAIN WILD-TYPE 174 155  72  83
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               26                174
  N1               27                155
  N2               24                 72
  N3               14                 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"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    79   7
  11P GAIN WILD-TYPE 434  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     79    7
  11P GAIN WILD-TYPE  434   32
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               79                434
  1                7                 32
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    28  70
  11P GAIN WILD-TYPE 154 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     28   70
  11P GAIN WILD-TYPE  154  357
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               28                154
  MALE                 70                357
[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                                                 14
  11P GAIN WILD-TYPE                                               64
                    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                                14
  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                                  64
  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  97
  11P GAIN WILD-TYPE   5 506
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   97
  11P GAIN WILD-TYPE    5  506
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 1                  5
  YES               97                506
[1] 2 2
[1] FALSE
D21V10, continuous
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    48   2   5   4
  11P GAIN WILD-TYPE 299  16  14  21
D21V11, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               48                299
  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"
D21V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED      25                         4
  11P GAIN WILD-TYPE   104                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           1    58
  11P GAIN WILD-TYPE                                         0   327
D21V13, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                                   25                104
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   58                327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  55
  11P GAIN WILD-TYPE   6 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   55
  11P GAIN WILD-TYPE    6  339
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               55                339
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    59  37
  11Q GAIN WILD-TYPE 295 184
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                96                479 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                37                184 
$`11Q GAIN MUTATED`
TCGA-IG-A51D TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A938 
       17.03        14.50       122.10        60.39         3.68        25.41 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OH TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A88Y 
        8.94        24.00        32.61         1.38        29.00         0.36 
TCGA-L5-A8NN TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR 
        5.49        13.41         5.92        12.46        12.33        13.22 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-V5-AASW 
        7.82         7.59         7.04        15.78         7.00         9.27 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN 
       22.82         8.12        30.71        19.73        11.01         9.44 
TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
       13.87        35.24         3.45        17.49        11.44         0.69 
TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8686 TCGA-BR-A4IY TCGA-CD-8525 
       15.58        19.50        15.81        15.68        12.89         0.07 
TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4444 
        0.10         9.34        12.20        20.02        54.08        47.05 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5722 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 
       12.00        30.97         0.99        17.19        15.22        14.66 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 TCGA-HU-8243 
       11.24         2.96         7.99        72.23        17.06         5.92 
TCGA-HU-A4G2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RO 
       24.30        12.30        27.42         3.39         5.36         1.41 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZI 
        6.74         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-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91Y 
       14.33        11.93        18.74        22.68         1.71         9.73 
TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-ZQ-A9CR 
        4.54        40.08        32.94        29.98        54.12         0.79 

$`11Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        42.77        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        0.30         4.31         3.68         4.70        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37         8.71        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        11.54         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       12.00        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         8.02         5.06        14.70        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
       53.95         9.30         2.89         1.45        12.69        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
       20.38         5.29         3.42         4.80        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       18.81        19.96        12.43         1.55        18.31        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        42.87        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 
       15.91        10.16         3.42         2.10         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.70        19.56         9.47         6.61         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-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        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-7957 TCGA-BR-7958 
       18.15        15.32        28.73        12.43         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       18.71        14.43        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-8297 
        0.56        12.95         2.66        16.31         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        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-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        12.79         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-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-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-8526 TCGA-CD-8527 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.07         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-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        3.42        11.31        12.43        11.61         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-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-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       21.99         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-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-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-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        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-D7-8578 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-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-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-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-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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        23.84         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.45        18.81        18.38         5.19        13.08         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
       12.59         6.51         7.82        13.51         2.53        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       20.15         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52         6.08         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-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-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-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-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q 
       27.35        65.16        36.69        11.70        61.22        20.81 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       36.16         7.36         9.50        52.24         9.04         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-AA69 TCGA-VQ-AA6D 
       42.54        11.24        22.09        18.41        28.41        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        21.11        12.43        10.62 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.07               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             122.1              122.3 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.12              12.69 
[1] "0.1 - 122.1 (13.1)" "0.0 - 122.3 (12.7)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         3        3        7        2         8        18
  11Q GAIN WILD-TYPE       8       16       41       30        69        66
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           4         16         15          9        9
  11Q GAIN WILD-TYPE        25         81         57         39       42
                    vv
clus                 STAGE IVA
  11Q GAIN MUTATED           1
  11Q GAIN WILD-TYPE         3
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  3                 16
  STAGE IB                  7                 41
  STAGE II                  2                 30
  STAGE IIA                 8                 69
  STAGE IIB                18                 66
  STAGE III                 4                 25
  STAGE IIIA               16                 81
  STAGE IIIB               15                 57
  STAGE IIIC                9                 39
  STAGE IV                  9                 42
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11Q GAIN MUTATED       9  16  48  24
  11Q GAIN WILD-TYPE    44 110 232 100
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                9                 44
  T2                  16                110
  T3                  48                232
  T4                  24                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
  11Q GAIN MUTATED    27  28  28  12
  11Q GAIN WILD-TYPE 173 154  68  85
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               27                173
  N1               28                154
  N2               28                 68
  N3               12                 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"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    87   5
  11Q GAIN WILD-TYPE 426  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     87    5
  11Q GAIN WILD-TYPE  426   34
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               87                426
  1                5                 34
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    34  69
  11Q GAIN WILD-TYPE 148 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     34   69
  11Q GAIN WILD-TYPE  148  358
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               34                148
  MALE                 69                358
[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     1 102
  11Q GAIN WILD-TYPE   5 501
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1  102
  11Q GAIN WILD-TYPE    5  501
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 1                  5
  YES              102                501
[1] 2 2
[1] FALSE
D22V10, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    58   2   6   4
  11Q GAIN WILD-TYPE 289  16  13  21
D22V11, 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"
D22V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED      22                         4
  11Q GAIN WILD-TYPE   107                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           1    64
  11Q GAIN WILD-TYPE                                         0   321
D22V13, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                                   22                107
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   64                321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  60
  11Q GAIN WILD-TYPE   6 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   60
  11Q GAIN WILD-TYPE    6  334
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               60                334
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    90  47
  12P GAIN WILD-TYPE 264 174
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               137                438 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                47                174 
$`12P GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L 
        7.63        16.24        20.09         2.63        18.64         0.53 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI 
       23.41         4.67         0.30         4.31        24.00        19.99 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A8NF TCGA-L5-A8NL 
       47.93         3.32         4.90         0.36         2.66        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        5.49        21.37        27.12        10.36         5.92        10.45 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 
        0.10        13.15         0.10        13.25        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.59         0.10        15.52        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG 
       25.25        13.18         0.13         8.02         7.59        29.59 
TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU 
       53.95        12.69        20.38        19.96         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-Z6-AAPN TCGA-B7-A5TK TCGA-BR-6563 
        8.12        28.11        42.87         2.66         9.47        39.12 
TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8078 
       32.78        12.16        21.11        28.73        18.71        12.26 
TCGA-BR-8295 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8381 
        2.20        19.50         0.26         0.95         3.32         0.26 
TCGA-BR-8486 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 
       20.22         1.48         0.72         1.15         2.83         3.25 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
        0.07         0.16         0.10        47.05        21.99        22.98 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 
        0.99        12.03        79.07        12.66        19.13        18.54 
TCGA-D7-6526 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A6EX TCGA-D7-A6F0 
       17.19        11.31        19.50         5.92        11.31         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7735 
       15.65         8.38         7.40        16.24        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
       19.53        22.29         5.52         1.51        14.17        12.10 
TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GT 
       24.30         3.25        22.75        25.81         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ 
        6.25        10.19        27.42         3.45         3.39         5.36 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H 
        6.44         6.74         7.82         2.53        60.56        37.64 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT 
       18.21        61.25         6.08         8.94         5.79        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A91A 
       13.25        18.48        21.73         7.73        22.19        36.69 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A928 TCGA-VQ-AA6K 
       11.93        20.81        36.16         5.72        12.43 

$`12P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
        8.94         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        0.85        20.78        20.12         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        0.79        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         8.94         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        4.70        32.61        21.01        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         8.71        13.41        83.24        52.57        46.09 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       12.66        12.43        13.41        15.35         0.10        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HW 
       12.49        22.39        11.54        12.33        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6KZ 
       12.23        12.03        33.11         5.16         7.82         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       14.70         7.04         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        1.45         7.00        20.02         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         4.44        18.81        22.82        12.43 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 
       15.91        10.16         3.42         2.10        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56        11.01         9.44         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-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-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        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-8058 
       15.32        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        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-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
        6.18        13.08        22.19        17.52        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 
       14.04        11.80        19.17        14.79        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-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       12.56        13.87         7.53         6.08        22.26        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-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       13.64        11.57         5.13        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
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-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02       105.07        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 
       69.04        21.07         7.99        12.36        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.61        17.85        13.35        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-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       11.44         9.76         4.34         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 
       14.47        72.23        21.27        14.07        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-A4GH TCGA-HU-A4GJ 
        5.59        12.30        11.84        24.20        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
       29.98         0.10         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-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS 
       18.81        18.38         5.19        13.08         1.41        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93G 
        6.51         5.56         1.81        13.51         5.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A804 
        3.72        19.73         9.86        45.67         8.52         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-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       35.61        16.87        19.04         0.92         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       35.24        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       46.26        16.31         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K 
       27.35        64.57        14.33        65.16        11.70        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        22.68         1.71         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-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-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        21.11        10.62         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 
             12.10              12.95 
[1] "0.1 - 79.1 (12.1)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1"  
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         0        3        8        5        26        20
  12P GAIN WILD-TYPE      11       16       40       27        51        64
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED          10         25         15         10       11
  12P GAIN WILD-TYPE        19         72         57         38       40
                    vv
clus                 STAGE IVA
  12P GAIN MUTATED           3
  12P GAIN WILD-TYPE         1
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                 11
  STAGE IA                  3                 16
  STAGE IB                  8                 40
  STAGE II                  5                 27
  STAGE IIA                26                 51
  STAGE IIB                20                 64
  STAGE III                10                 19
  STAGE IIIA               25                 72
  STAGE IIIB               15                 57
  STAGE IIIC               10                 38
  STAGE IV                 11                 40
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12P GAIN MUTATED      10  25  83  19
  12P GAIN WILD-TYPE    43 101 197 105
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               10                 43
  T2                  25                101
  T3                  83                197
  T4                  19                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
  12P GAIN MUTATED    48  41  28  19
  12P GAIN WILD-TYPE 152 141  68  78
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               48                152
  N1               41                141
  N2               28                 68
  N3               19                 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"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   114  12
  12P GAIN WILD-TYPE 399  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    114   12
  12P GAIN WILD-TYPE  399   27
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0              114                399
  1               12                 27
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    34 108
  12P GAIN WILD-TYPE 148 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     34  108
  12P GAIN WILD-TYPE  148  319
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               34                148
  MALE                108                319
[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     0 142
  12P GAIN WILD-TYPE   6 461
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0  142
  12P GAIN WILD-TYPE    6  461
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 0                  6
  YES              142                461
[1] 2 2
[1] FALSE
D23V10, continuous
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    74   4   4   1
  12P GAIN WILD-TYPE 273  14  15  24
D23V11, 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"
D23V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED      41                         3
  12P GAIN WILD-TYPE    88                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           0    84
  12P GAIN WILD-TYPE                                         1   301
D23V13, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                                   41                 88
  BLACK OR AFRICAN AMERICAN                                3                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   84                301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     3  96
  12P GAIN WILD-TYPE   4 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   96
  12P GAIN WILD-TYPE    4  298
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               96                298
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    71  39
  12Q GAIN WILD-TYPE 283 182
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               110                465 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                39                182 
$`12Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A4OE 
        7.63        16.24         2.63         0.53         4.67        24.00 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A8NL TCGA-L5-A8NN 
       47.93         3.32         4.90         0.36        13.22         5.49 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A49W 
       27.12        52.57        10.36        10.45         0.10        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.59         0.10        15.52        11.54        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A9FO TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A8WG 
       12.33        25.25         0.13         7.59        29.59        12.69 
TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       19.96        18.31        28.11        42.87         2.66        19.73 
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-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
        8.94         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09         0.85        20.78        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         4.31         8.94         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        19.99        21.01        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55         7.76        21.37         8.71        13.41        83.24 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       46.09         5.92        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35         0.10        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.59        22.39        13.22        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        13.18        33.11         5.16         7.82         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        14.70         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       15.78         2.89         1.45         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY 
       18.81        22.82        12.43         1.55         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       10.16         3.42         2.10        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.44         6.61         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-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        19.33        26.10         9.17 
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-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-7851 
       23.93        15.42        28.01        18.15        15.32        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-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        16.31        15.58         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       13.08        22.19        17.52        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        19.17        14.79        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-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-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08        22.26        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         8.98        14.17        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-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13        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-8531 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C 
        0.10         0.13         0.10         3.42        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-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        7.99        12.36        11.93        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85        13.35        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       11.31        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-A4YX 
       14.66        21.14        20.91        14.27        16.44        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-A748 TCGA-D7-A74B TCGA-EQ-5647 
        9.76         2.96        15.65         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        0.23        18.08        26.47         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       11.41        10.62         0.76         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
        8.88         8.81        21.21        18.81        18.38         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-AB1X TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H 
        5.56         1.81        13.51         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-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-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-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        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-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       36.69        11.70        61.22        18.74        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-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58        64.18        21.04         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-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 

  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 
            10.405             13.150 
[1] "0.1 - 79.1 (10.4)"  "0.0 - 122.3 (13.2)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0        2        4        6        18        14
  12Q GAIN WILD-TYPE      11       17       44       26        59        70
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           7         21         15          7       12
  12Q GAIN WILD-TYPE        22         76         57         41       39
                    vv
clus                 STAGE IVA
  12Q GAIN MUTATED           2
  12Q GAIN WILD-TYPE         2
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                 11
  STAGE IA                  2                 17
  STAGE IB                  4                 44
  STAGE II                  6                 26
  STAGE IIA                18                 59
  STAGE IIB                14                 70
  STAGE III                 7                 22
  STAGE IIIA               21                 76
  STAGE IIIB               15                 57
  STAGE IIIC                7                 41
  STAGE IV                 12                 39
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12Q GAIN MUTATED       7  18  65  19
  12Q GAIN WILD-TYPE    46 108 215 105
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                7                 46
  T2                  18                108
  T3                  65                215
  T4                  19                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
  12Q GAIN MUTATED    31  35  27  15
  12Q GAIN WILD-TYPE 169 147  69  82
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               31                169
  N1               35                147
  N2               27                 69
  N3               15                 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"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    90  11
  12Q GAIN WILD-TYPE 423  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     90   11
  12Q GAIN WILD-TYPE  423   28
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               90                423
  1               11                 28
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    27  85
  12Q GAIN WILD-TYPE 155 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     27   85
  12Q GAIN WILD-TYPE  155  342
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               27                155
  MALE                 85                342
[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     0 112
  12Q GAIN WILD-TYPE   6 491
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0  112
  12Q GAIN WILD-TYPE    6  491
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 0                  6
  YES              112                491
[1] 2 2
[1] FALSE
D24V10, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    60   3   4   2
  12Q GAIN WILD-TYPE 287  15  15  23
D24V11, 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"
D24V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED      37                         1
  12Q GAIN WILD-TYPE    92                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           0    60
  12Q GAIN WILD-TYPE                                         1   325
D24V13, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                                   37                 92
  BLACK OR AFRICAN AMERICAN                                1                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   60                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     3  76
  12Q GAIN WILD-TYPE   4 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   76
  12Q GAIN WILD-TYPE    4  318
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               76                318
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED   115  66
  13Q GAIN WILD-TYPE 239 155
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               181                394 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                66                155 
$`13Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A5B8 TCGA-IG-A97H 
       31.27        14.30         5.92        13.94         0.79        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C 
      122.10         3.68        42.77        23.18        31.56         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OP TCGA-L5-A4OQ 
       30.25         8.94         4.70        19.99         7.17         1.38 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        7.13         2.60         0.36         3.02         2.66        12.92 
TCGA-L5-A8NT TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-Q9-A6FW TCGA-R6-A6L4 
       27.12        12.33        25.25        12.00         7.82        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB 
        7.04        29.59         9.30        15.78        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         9.27        46.19        10.16        19.73        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       11.01         9.44         4.64         9.57         6.61        15.95 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-7197 
       39.12         9.17        32.78        25.61        21.11         9.21 
TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       35.24        18.15        28.73         0.69        12.26         9.60 
TCGA-BR-8286 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 
       12.95        13.08        14.79        15.85         5.39         9.21 
TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       12.79        11.54        16.44        15.68         8.22        10.68 
TCGA-BR-A44U TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 
       13.87         0.72        14.17        12.82        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
       20.65        20.42         1.15         5.13         3.25        13.15 
TCGA-CD-8529 TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 
        0.13         0.13        12.43         6.58        12.20        20.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4469 TCGA-CG-4472 
       15.95         7.99        54.08        47.05         7.07        12.00 
TCGA-CG-5719 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        1.02         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       19.13        18.54        17.85        17.19        10.26        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-A4YT TCGA-D7-A4Z0 
       10.55        11.31        19.50        17.19        14.27        14.76 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-EQ-5647 TCGA-EQ-8122 
       11.24         2.96        15.65         8.38         0.62         7.99 
TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       72.23        19.53         5.52        12.59        14.17        12.10 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU 
       12.30        11.84        22.75        25.81         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI 
        0.26        19.36        23.84        12.30        27.42        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
        5.19         1.41         6.44         1.81         5.56        37.64 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A8MV 
        9.86        45.67        18.21         8.52         8.61       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-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        21.73        34.45 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PY 
       22.19         2.70        17.85        23.41        13.35        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       65.16        36.69        20.81        22.68         1.71        36.16 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6J 
        9.04        21.04        42.54        11.24        29.98        21.11 
TCGA-VQ-AA6K 
       12.43 

$`13Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        58.55         7.63         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       32.45         7.69         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG 
        4.67        12.16        44.75        60.39        68.02        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H 
       25.41        21.70        25.22        24.03         6.28         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        4.31        24.00         3.68        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         3.16        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43         6.94         8.71        25.12         7.40         3.95 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50        35.97        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.59        22.39         0.10        15.52        11.54        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        10.52        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        33.11         5.16         8.02         7.59         5.06 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35        53.95         2.89         1.45        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38         4.80        15.35         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        42.87        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI 
       15.91         3.42         2.10         2.66        26.70        19.56 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         6.61         6.97         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.18        34.68        13.87        17.29        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       26.10        18.05        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        32.94        12.82        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       28.01        15.32        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8284 
       18.71        17.49        14.43        11.44        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-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-8381 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
        0.26         3.72        25.18        20.22         1.12        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-8683 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86        12.56         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.41        13.51        12.89         8.98         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
       19.36        13.64        11.57         2.83        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-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 
              0.13               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            122.30             116.38 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            12.820             12.725 
[1] "0.1 - 122.3 (12.8)" "0.0 - 116.4 (12.7)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         6        4       11       11        17        26
  13Q GAIN WILD-TYPE       5       15       37       21        60        58
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           6         33         22         15       21
  13Q GAIN WILD-TYPE        23         64         50         33       30
                    vv
clus                 STAGE IVA
  13Q GAIN MUTATED           2
  13Q GAIN WILD-TYPE         2
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   6                  5
  STAGE IA                  4                 15
  STAGE IB                 11                 37
  STAGE II                 11                 21
  STAGE IIA                17                 60
  STAGE IIB                26                 58
  STAGE III                 6                 23
  STAGE IIIA               33                 64
  STAGE IIIB               22                 50
  STAGE IIIC               15                 33
  STAGE IV                 21                 30
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  13Q GAIN MUTATED      18  41  81  40
  13Q GAIN WILD-TYPE    35  85 199  84
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               18                 35
  T2                  41                 85
  T3                  81                199
  T4                  40                 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
  13Q GAIN MUTATED    52  54  37  34
  13Q GAIN WILD-TYPE 148 128  59  63
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               52                148
  N1               54                128
  N2               37                 59
  N3               34                 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"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   160  13
  13Q GAIN WILD-TYPE 353  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    160   13
  13Q GAIN WILD-TYPE  353   26
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0              160                353
  1               13                 26
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    52 140
  13Q GAIN WILD-TYPE 130 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     52  140
  13Q GAIN WILD-TYPE  130  287
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               52                130
  MALE                140                287
[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                                                       54
  13Q GAIN WILD-TYPE                                                    108
                    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                                                          9
  13Q GAIN WILD-TYPE                                                       12
                    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)                          54
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         9
  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)                           108
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          12
  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     1 191
  13Q GAIN WILD-TYPE   5 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1  191
  13Q GAIN WILD-TYPE    5  412
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 1                  5
  YES              191                412
[1] 2 2
[1] FALSE
D25V10, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED   117   8   6   9
  13Q GAIN WILD-TYPE 230  10  13  16
D25V11, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0              117                230
  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"
D25V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED      35                         7
  13Q GAIN WILD-TYPE    94                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           1   120
  13Q GAIN WILD-TYPE                                         0   265
D25V13, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                                   35                 94
  BLACK OR AFRICAN AMERICAN                                7                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  120                265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     3 124
  13Q GAIN WILD-TYPE   4 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3  124
  13Q GAIN WILD-TYPE    4  270
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              124                270
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    38  31
  14Q GAIN WILD-TYPE 316 190
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                69                506 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                31                190 
$`14Q GAIN MUTATED`
TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A6QS TCGA-IG-A97I 
        5.92         0.85        20.78        18.64         9.96        12.16 
TCGA-JY-A6FG TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OX 
       41.52        23.18         3.16        30.25         4.31         7.43 
TCGA-L5-A8NG TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49S 
       35.97         5.49        21.37        13.41         5.92        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A9 
       15.35         0.10         0.10        12.59        12.59        11.54 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       13.22        12.33        25.25        12.03        13.18         0.13 
TCGA-R6-A6DN TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASX TCGA-VR-A8EW 
        8.02        53.95        20.02        20.38         4.44         8.12 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       46.19        11.24         9.17        15.91         3.42        19.73 
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-A48A TCGA-CG-4444 TCGA-CG-4460 TCGA-D7-6518 TCGA-D7-A6F2 TCGA-EQ-5647 
       12.43        47.05        21.99        19.13        15.65         0.62 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A7NR TCGA-IN-A7NT 
        5.52         5.92        18.38         1.41         6.51         5.56 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A7BS TCGA-VQ-A8PE TCGA-VQ-A91V TCGA-VQ-A925 
       45.67         8.52        11.05        22.19        36.16         4.54 
TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6I 
       42.54        40.08        16.14 

$`14Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
       33.27        20.09         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
        0.53        17.03         0.79        23.41        12.82        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        4.67        14.50       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
        3.68        42.77        25.41        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       24.03         6.28         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        0.36         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W 
       10.45        12.66        12.43        13.41         0.10        13.25 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.49        12.76        22.39         0.10        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-M9-A5M8 
       12.33         4.47        10.52        12.00        12.23        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       29.59         6.35         9.30        15.78         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00         5.29         3.42         4.80        15.35 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       18.31        28.11        30.71        18.18        42.87        15.06 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       10.16         2.10         2.66        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        32.78        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-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-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-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-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-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       19.36         0.46        20.65         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-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-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-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-D7-6519 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-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44         9.76         2.96         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         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-8211 TCGA-FP-8631 TCGA-FP-A8CX 
       17.06        59.54         5.03        13.58         0.56         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       18.08        26.47         1.51        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-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-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-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-A6RS TCGA-IN-A7NU TCGA-IN-AB1V 
       13.08         6.44         6.74        12.59         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-A7ZI TCGA-R5-A7ZR 
        3.72        19.73         9.86        18.21        61.25         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60         9.24         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        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-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-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-A91Z TCGA-VQ-A922 
        1.71         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-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        11.24        22.09        18.41        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        17.13        54.12        26.04        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               0.1                0.0 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             53.95             122.30 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             12.59              12.79 
[1] "0.1 - 54.0 (12.6)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         2        1        4        0        14        10
  14Q GAIN WILD-TYPE       9       18       44       32        63        74
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           7         10          6          5        7
  14Q GAIN WILD-TYPE        22         87         66         43       44
                    vv
clus                 STAGE IVA
  14Q GAIN MUTATED           0
  14Q GAIN WILD-TYPE         4
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   2                  9
  STAGE IA                  1                 18
  STAGE IB                  4                 44
  STAGE II                  0                 32
  STAGE IIA                14                 63
  STAGE IIB                10                 74
  STAGE III                 7                 22
  STAGE IIIA               10                 87
  STAGE IIIB                6                 66
  STAGE IIIC                5                 43
  STAGE IV                  7                 44
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  14Q GAIN MUTATED       4  18  33  11
  14Q GAIN WILD-TYPE    49 108 247 113
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                4                 49
  T2                  18                108
  T3                  33                247
  T4                  11                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
  14Q GAIN MUTATED    27  18   8  13
  14Q GAIN WILD-TYPE 173 164  88  84
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               27                173
  N1               18                164
  N2                8                 88
  N3               13                 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"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    57   6
  14Q GAIN WILD-TYPE 456  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     57    6
  14Q GAIN WILD-TYPE  456   33
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               57                456
  1                6                 33
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    13  58
  14Q GAIN WILD-TYPE 169 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     13   58
  14Q GAIN WILD-TYPE  169  369
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               13                169
  MALE                 58                369
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  14Q GAIN MUTATED                                       3
  14Q GAIN WILD-TYPE                                    68
                    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                                            3
  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                                             68
  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  71
  14Q GAIN WILD-TYPE   6 532
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   71
  14Q GAIN WILD-TYPE    6  532
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 0                  6
  YES               71                532
[1] 2 2
[1] FALSE
D26V10, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    19   2   3   1
  14Q GAIN WILD-TYPE 328  16  16  24
D26V11, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               19                328
  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"
D26V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED      20                         1
  14Q GAIN WILD-TYPE   109                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           0    45
  14Q GAIN WILD-TYPE                                         1   340
D26V13, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                                   20                109
  BLACK OR AFRICAN AMERICAN                                1                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   45                340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  46
  14Q GAIN WILD-TYPE   6 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   46
  14Q GAIN WILD-TYPE    6  348
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               46                348
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    30  32
  15Q GAIN WILD-TYPE 324 189
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                62                513 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                32                189 
$`15Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IG-A50L TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43C 
        7.63         8.94         0.53       122.10        60.39         3.16 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NJ 
        3.16         7.13         6.94         2.60         0.36        16.47 
TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4MR TCGA-LN-A7HW TCGA-LN-A7HX 
       46.09        10.45         0.10        13.22        12.00        12.23 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-VR-A8EP 
       33.11         7.82         7.59         7.04         6.35        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-AA7D TCGA-BR-4183 TCGA-BR-6709 TCGA-BR-7197 
       22.82         1.55         9.17         6.61        12.16         9.21 
TCGA-BR-7959 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-A486 
       18.71         9.86         8.22         1.15         3.25         3.42 
TCGA-CG-4477 TCGA-CG-5727 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6815 TCGA-EQ-5647 
       30.97        79.07        18.84        13.35        15.98         0.62 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-HU-A4GH TCGA-IN-7808 TCGA-IN-8663 
       72.23        11.38        17.06        11.77         3.45         3.39 
TCGA-IN-A6RO TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT 
        1.41        60.56        37.64        18.21         6.08         8.61 
TCGA-RD-A8MV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ 
      122.30        13.02        18.48        46.26        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A925 
       17.85         4.54 

$`15Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       16.24         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         1.38        58.59         4.90        29.00         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        8.71        25.12         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        11.54        12.33         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU 
       25.25        10.52        12.03        13.18         0.13         5.16 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         5.06        14.70        29.59        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
        4.44        18.81        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10         2.66        19.73 
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-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-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-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-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-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        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-D7-6527 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-D7-8576 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-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
        7.40         7.13         7.99        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-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-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-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        9.67         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38         5.36         5.19        13.08         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-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53         5.56        20.15         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       45.67         8.52        61.25         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 
        5.79         0.92        48.79         5.46        13.25        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-A8PM TCGA-VQ-A8PO 
       34.29        16.31        22.19         2.50         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-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-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        22.68         1.71        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-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-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-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 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               0.1                0.0 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            122.30             116.38 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            10.155             12.890 
[1] "0.1 - 122.3 (10.2)" "0.0 - 116.4 (12.9)"
[1] "hr=" "1.4"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         2        4        4        3         9         4
  15Q GAIN WILD-TYPE       9       15       44       29        68        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           8          9          8          3        5
  15Q GAIN WILD-TYPE        21         88         64         45       46
                    vv
clus                 STAGE IVA
  15Q GAIN MUTATED           0
  15Q GAIN WILD-TYPE         4
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  9
  STAGE IA                  4                 15
  STAGE IB                  4                 44
  STAGE II                  3                 29
  STAGE IIA                 9                 68
  STAGE IIB                 4                 80
  STAGE III                 8                 21
  STAGE IIIA                9                 88
  STAGE IIIB                8                 64
  STAGE IIIC                3                 45
  STAGE IV                  5                 46
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  15Q GAIN MUTATED       7  14  30   9
  15Q GAIN WILD-TYPE    46 112 250 115
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1                7                 46
  T2                  14                112
  T3                  30                250
  T4                   9                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
  15Q GAIN MUTATED    20  15  15   9
  15Q GAIN WILD-TYPE 180 167  81  88
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               20                180
  N1               15                167
  N2               15                 81
  N3                9                 88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    50   5
  15Q GAIN WILD-TYPE 463  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     50    5
  15Q GAIN WILD-TYPE  463   34
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               50                463
  1                5                 34
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    13  51
  15Q GAIN WILD-TYPE 169 376
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13   51
  15Q GAIN WILD-TYPE  169  376
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               13                169
  MALE                 51                376
[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                                                       11
  15Q GAIN WILD-TYPE                                                    151
                    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                                                          1
  15Q GAIN WILD-TYPE                                                       20
                    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)                          11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  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)                           151
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 72
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  68
  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"
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  64
  15Q GAIN WILD-TYPE   6 539
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   64
  15Q GAIN WILD-TYPE    6  539
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  6
  YES               64                539
[1] 2 2
[1] FALSE
D27V10, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    22   3   6   1
  15Q GAIN WILD-TYPE 325  15  13  24
D27V11, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               22                325
  R1                3                 15
  R2                6                 13
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED      13                         4
  15Q GAIN WILD-TYPE   116                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           1    35
  15Q GAIN WILD-TYPE                                         0   350
D27V13, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                                   13                116
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   35                350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  34
  15Q GAIN WILD-TYPE   7 360
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   34
  15Q GAIN WILD-TYPE    7  360
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               34                360
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    55  35
  16P GAIN WILD-TYPE 299 186
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                90                485 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                35                186 
$`16P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-IG-A97H 
       58.55         0.85         0.53         0.79         4.67        14.50 
TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NF 
        0.30         3.32        29.00         6.94        55.50         2.66 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49S 
       21.37        13.41        27.12        10.36         5.92        13.15 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
       13.25        12.59        12.76        12.59         0.10        11.54 
TCGA-LN-A5U6 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W5 
       12.33        12.03         0.13         5.06        29.59        15.78 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-Z6-A8JD 
       20.38        15.35        12.43         8.12        28.11         3.42 
TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-6456 TCGA-BR-6565 
       19.73        11.01         9.44         4.64        17.29         9.17 
TCGA-BR-8080 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4J5 TCGA-BR-A4J8 
        9.60        25.18        20.22         7.53        12.82        13.51 
TCGA-BR-A4PD TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8529 TCGA-CG-4438 TCGA-CG-4444 
       20.65        13.18         0.10         0.13        54.08        47.05 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5719 TCGA-CG-5722 
       21.99         0.00        12.00        22.98         1.02         0.99 
TCGA-CG-5730 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8576 
        4.01        18.54        17.19        12.79        10.55        14.66 
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-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        3.16        58.59         4.90         7.13         7.43         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         5.49         8.71        83.24        52.57        46.09 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.45        12.66        12.43        13.41         0.10        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.10        12.46        12.49        22.39        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.23        13.18        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        2.89         1.45        12.69         7.00        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42         4.80         9.27         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       22.82         1.55        18.31        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        2.10         2.66        26.70        11.70        19.56         9.47 
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-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-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-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        12.26        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-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-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.42         1.15        13.64        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-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.07         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-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-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02       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-D7-6518 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-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
       17.85        13.35        10.26        15.22        15.98        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-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-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-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-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         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-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
        3.45        18.81        18.38         5.36        13.08         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.59         6.51         7.82        13.51         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-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-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-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-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        26.24        27.35        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-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        22.68         1.71        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-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-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       11.24        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        21.11        10.62         0.79 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.00               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             58.55             122.30 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             12.18              12.92 
[1] "0.0 - 58.5 (12.2)"  "0.1 - 122.3 (12.9)"
[1] "hr=" "1.3"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         1        2        5        1        11        14
  16P GAIN WILD-TYPE      10       17       43       31        66        70
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           6         22          6         10       10
  16P GAIN WILD-TYPE        23         75         66         38       41
                    vv
clus                 STAGE IVA
  16P GAIN MUTATED           3
  16P GAIN WILD-TYPE         1
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   1                 10
  STAGE IA                  2                 17
  STAGE IB                  5                 43
  STAGE II                  1                 31
  STAGE IIA                11                 66
  STAGE IIB                14                 70
  STAGE III                 6                 23
  STAGE IIIA               22                 75
  STAGE IIIB                6                 66
  STAGE IIIC               10                 38
  STAGE IV                 10                 41
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16P GAIN MUTATED       6  17  46  22
  16P GAIN WILD-TYPE    47 109 234 102
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                6                 47
  T2                  17                109
  T3                  46                234
  T4                  22                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
  16P GAIN MUTATED    29  27  15  17
  16P GAIN WILD-TYPE 171 155  81  80
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               29                171
  N1               27                155
  N2               15                 81
  N3               17                 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"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    71   9
  16P GAIN WILD-TYPE 442  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     71    9
  16P GAIN WILD-TYPE  442   30
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               71                442
  1                9                 30
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    20  75
  16P GAIN WILD-TYPE 162 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     20   75
  16P GAIN WILD-TYPE  162  352
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               20                162
  MALE                 75                352
[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                                                       24
  16P GAIN WILD-TYPE                                                    138
                    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)                          24
  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)                           138
  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  92
  16P GAIN WILD-TYPE   3 511
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   92
  16P GAIN WILD-TYPE    3  511
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 3                  3
  YES               92                511
[1] 2 2
[1] FALSE
D28V10, continuous
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    44   1   6   3
  16P GAIN WILD-TYPE 303  17  13  22
D28V11, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               44                303
  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"
D28V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED      26                         2
  16P GAIN WILD-TYPE   103                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           1    53
  16P GAIN WILD-TYPE                                         0   332
D28V13, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                                   26                103
  BLACK OR AFRICAN AMERICAN                                2                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   53                332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  64
  16P GAIN WILD-TYPE   6 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   64
  16P GAIN WILD-TYPE    6  330
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               64                330
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    44  35
  16Q GAIN WILD-TYPE 310 186
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                79                496 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                35                186 
$`16Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-IG-A3Y9 TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A43J 
       13.94         0.85         0.79         4.67         0.30         4.31 
TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NF TCGA-L5-A8NQ TCGA-L5-A8NS 
        3.32        29.00         6.94         2.66        21.37        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A4A1 TCGA-LN-A4A3 
       27.12        52.57         0.10        13.15        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A7HY TCGA-LN-A9FO 
       12.59         0.10        11.54        12.33        12.03         0.13 
TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8ER 
       29.59        15.78        20.38         3.42        15.35        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA7B TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        8.12        28.11        11.24         3.42         2.10        19.73 
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-HU-A4GP TCGA-IN-8663 
       17.06         0.56         0.23        14.17         8.98         3.39 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-R5-A7ZE 
        1.41         6.44         6.74         5.56         1.81        18.21 
TCGA-RD-A7BT TCGA-VQ-A8DV TCGA-VQ-A8PS TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
        8.61        13.25        13.35        29.98        54.12        16.14 
TCGA-VQ-AA6K 
       12.43 

$`16Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16        30.25         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       32.61        19.99        21.01        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU 
       13.55        13.22         7.76         5.49         8.71        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.41        15.35         0.10        13.25         0.10        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.49        22.39        15.52        12.33        13.22         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 
       25.25        10.52        12.00        12.23        13.18        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.04         6.35        53.95         9.30         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
       12.69         7.00        20.02         5.29         4.80         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        22.82         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       30.71        18.18        42.87        46.19        15.06         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       15.91        10.16         2.66        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         6.97         7.43        18.35 
TCGA-BR-4201 TCGA-BR-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-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        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-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-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-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
        0.72        14.17         0.53         0.66        19.36         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-5802 TCGA-CD-5803 TCGA-CD-8524 
        2.83         3.25        13.15         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.07         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-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-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
        6.97        36.00         0.99         6.02       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        79.07        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        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-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        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-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-A4GY 
       29.98         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-7806 TCGA-IN-7808 TCGA-IN-8462 
        8.88         8.81        27.42        21.21         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR 
       18.38         5.36         5.19        13.08        12.59         6.51 
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-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-A7BW 
       61.25         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-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-A8DZ TCGA-VQ-A8E0 
        5.79         0.92        48.79         5.46        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        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-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-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       22.09        18.41        40.08        28.41        32.94        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        21.11        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 
             11.54              12.95 
[1] "0.0 - 54.1 (11.5)"  "0.1 - 122.3 (12.9)"
[1] "hr=" "1.7"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0        2        6        1        10        11
  16Q GAIN WILD-TYPE      11       17       42       31        67        73
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           6         15          5          9       11
  16Q GAIN WILD-TYPE        23         82         67         39       40
                    vv
clus                 STAGE IVA
  16Q GAIN MUTATED           3
  16Q GAIN WILD-TYPE         1
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                 11
  STAGE IA                  2                 17
  STAGE IB                  6                 42
  STAGE II                  1                 31
  STAGE IIA                10                 67
  STAGE IIB                11                 73
  STAGE III                 6                 23
  STAGE IIIA               15                 82
  STAGE IIIB                5                 67
  STAGE IIIC                9                 39
  STAGE IV                 11                 40
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16Q GAIN MUTATED       6  14  42  17
  16Q GAIN WILD-TYPE    47 112 238 107
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                6                 47
  T2                  14                112
  T3                  42                238
  T4                  17                107
[1] 4 2
[1] 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    28  23  11  16
  16Q GAIN WILD-TYPE 172 159  85  81
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               28                172
  N1               23                159
  N2               11                 85
  N3               16                 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"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    58  10
  16Q GAIN WILD-TYPE 455  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     58   10
  16Q GAIN WILD-TYPE  455   29
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               58                455
  1               10                 29
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    17  66
  16Q GAIN WILD-TYPE 165 361
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     17   66
  16Q GAIN WILD-TYPE  165  361
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               17                165
  MALE                 66                361
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16Q GAIN MUTATED                                       6
  16Q GAIN WILD-TYPE                                    65
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                       18
  16Q GAIN WILD-TYPE                                                    144
                    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                                            6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          18
  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                                             65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           144
  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  81
  16Q GAIN WILD-TYPE   4 522
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   81
  16Q GAIN WILD-TYPE    4  522
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 2                  4
  YES               81                522
[1] 2 2
[1] FALSE
D29V10, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    34   1   5   3
  16Q GAIN WILD-TYPE 313  17  14  22
D29V11, 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"
D29V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED      21                         3
  16Q GAIN WILD-TYPE   108                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           1    47
  16Q GAIN WILD-TYPE                                         0   338
D29V13, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                                   21                108
  BLACK OR AFRICAN AMERICAN                                3                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   47                338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  53
  16Q GAIN WILD-TYPE   6 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   53
  16Q GAIN WILD-TYPE    6  341
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               53                341
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    31  25
  17P GAIN WILD-TYPE 323 196
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                56                519 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                25                196 
$`17P GAIN MUTATED`
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-JY-A6FB TCGA-JY-A93C 
        7.69        20.09         0.53        17.03        60.39        23.18 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A88Z 
       25.22         0.30         4.31        18.35         1.38         7.40 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A4A2 
       55.50        35.97        13.41         0.10         0.10        12.49 
TCGA-LN-A4A4 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-V5-A7RC 
       12.59        12.33        12.00         8.02         5.06         3.42 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7I TCGA-Z6-A8JE 
        1.55        18.31        30.71        46.19        15.91         2.10 
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-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF 
       13.94         8.94        16.24         4.21        32.45         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M 
       31.56        24.03         6.28         3.16        30.25         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         3.32         7.17         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         0.36         3.95         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22         4.47        25.25        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
       13.18         0.13        33.11         5.16         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX 
       18.81        19.96        22.82        12.43         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       18.18        42.87        15.06        11.24         9.17        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-8077 
        3.45         9.07        12.76        18.71        17.49         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-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-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-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-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-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       19.07         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-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-D7-5579 
       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-D7-6815 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        15.98        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       11.31        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-A6EX 
       15.16        13.78        14.76        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-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.13         7.99        14.47        21.27        11.38         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-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-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-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-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-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-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73         9.86        45.67        18.21         8.52        61.25 
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-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-A91X 
       20.81        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        9.73        55.43         6.58         5.72        64.18         2.66 
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-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 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               0.1                0.0 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             72.23             122.30 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             13.10              12.76 
[1] "0.1 - 72.2 (13.1)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         1        1        2        1        11        11
  17P GAIN WILD-TYPE      10       18       46       31        66        73
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           7          9          4          1        7
  17P GAIN WILD-TYPE        22         88         68         47       44
                    vv
clus                 STAGE IVA
  17P GAIN MUTATED           0
  17P GAIN WILD-TYPE         4
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   1                 10
  STAGE IA                  1                 18
  STAGE IB                  2                 46
  STAGE II                  1                 31
  STAGE IIA                11                 66
  STAGE IIB                11                 73
  STAGE III                 7                 22
  STAGE IIIA                9                 88
  STAGE IIIB                4                 68
  STAGE IIIC                1                 47
  STAGE IV                  7                 44
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17P GAIN MUTATED       7  11  29   9
  17P GAIN WILD-TYPE    46 115 251 115
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1                7                 46
  T2                  11                115
  T3                  29                251
  T4                   9                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
  17P GAIN MUTATED    16  26   7   5
  17P GAIN WILD-TYPE 184 156  89  92
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               16                184
  N1               26                156
  N2                7                 89
  N3                5                 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"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    45   5
  17P GAIN WILD-TYPE 468  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     45    5
  17P GAIN WILD-TYPE  468   34
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               45                468
  1                5                 34
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    11  48
  17P GAIN WILD-TYPE 171 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     11   48
  17P GAIN WILD-TYPE  171  379
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               11                171
  MALE                 48                379
[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  58
  17P GAIN WILD-TYPE   5 545
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   58
  17P GAIN WILD-TYPE    5  545
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 1                  5
  YES               58                545
[1] 2 2
[1] FALSE
D30V10, continuous
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    21   0   5   1
  17P GAIN WILD-TYPE 326  18  14  24
D30V11, 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"
D30V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED      13                         4
  17P GAIN WILD-TYPE   116                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0    36
  17P GAIN WILD-TYPE                                         1   349
D30V13, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                                   13                116
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   36                349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  33
  17P GAIN WILD-TYPE   7 361
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   33
  17P GAIN WILD-TYPE    7  361
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               33                361
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    60  38
  17Q GAIN WILD-TYPE 294 183
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                98                477 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                38                183 
$`17Q GAIN MUTATED`
TCGA-2H-A9GF TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A6FB 
       25.78        20.09         0.53        17.03        12.82        60.39 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE 
       23.18        31.56        25.22        30.25         0.30        24.00 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A88Z TCGA-L5-A8NE 
       18.35         3.32         1.38         4.90         7.40        55.50 
TCGA-L5-A8NG TCGA-L5-A8NN TCGA-L5-A8NT TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
       35.97         5.49        27.12         0.10        13.15         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-R6-A6DN 
       12.49        12.76        12.59        12.33        12.00         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
        7.59         5.06        29.59         3.42        15.35         9.27 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7I TCGA-Z6-A8JE 
        1.55        18.31        30.71        46.19        15.91         2.10 
TCGA-B7-5818 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 
       11.70        14.43        11.44        12.95         2.66        14.04 
TCGA-BR-8686 TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-A486 
       15.68        12.89         0.53        20.42        13.64         3.42 
TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5719 TCGA-CG-5722 
        7.99        12.03        21.99        22.98         1.02         0.99 
TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8573 TCGA-D7-A6EY 
       12.03        18.54        13.35        12.79        19.50        11.44 
TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-7916 
        2.96         0.62        16.24        72.23        19.53        14.07 
TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
       26.47        12.10        27.42        18.81        18.38         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-R5-A7ZR 
        1.41         6.44         5.56         1.81         7.82         6.08 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91V 
       13.25        13.02        18.48        65.16        20.81        36.16 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O 
       52.24         9.04         2.01         4.54        64.18        21.04 
TCGA-VQ-A94R TCGA-VQ-AA68 
       42.54        40.08 

$`17Q GAIN WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        3.88         9.30         0.79        23.41         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93F 
        3.68        41.52        42.77        25.41        21.70        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        6.28         3.16         4.31         8.94         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
       32.61        19.99        21.01        47.93         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       58.59        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         0.36         3.95         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 
       15.35        13.25         0.10        12.46        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        10.52        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
       33.11         5.16         7.82        14.70         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASX 
        7.00        20.02        20.38         5.29         4.80         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX 
       18.81        19.96        22.82        12.43         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       18.18        42.87        15.06        11.24         9.17        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
        3.42         2.66        19.73        26.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-8077 TCGA-BR-8078 
        9.07        12.76        18.71        17.49         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
        9.60        20.55         8.05         0.56        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-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-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-8687 TCGA-BR-8690 
       11.54        15.81        16.44         9.86         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-A4J5 
       13.41        13.51         8.98         0.72        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.66        19.36        13.51         0.46        20.65         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       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-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-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-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-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02       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-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       17.85        17.19        10.26        15.22        15.98        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       11.31        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-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
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-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 
        7.99        14.47        21.27        11.38         3.48        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        0.23        18.08         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-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
        3.45         3.39         5.36        13.08         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        6.51        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-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        61.25         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 
       19.04         5.79         0.92        48.79         5.46        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-A8PY TCGA-VQ-A91A 
       13.35        26.24        27.35        64.57        14.33        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-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        7.36         9.50         9.73        55.43         6.58         5.72 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        11.24        22.09        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 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               0.1                0.0 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             72.23             122.30 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            12.985             12.620 
[1] "0.1 - 72.2 (13.0)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1"  
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         3        3        8        3        12        13
  17Q GAIN WILD-TYPE       8       16       40       29        65        71
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED          10         15          8          7       12
  17Q GAIN WILD-TYPE        19         82         64         41       39
                    vv
clus                 STAGE IVA
  17Q GAIN MUTATED           0
  17Q GAIN WILD-TYPE         4
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  3                 16
  STAGE IB                  8                 40
  STAGE II                  3                 29
  STAGE IIA                12                 65
  STAGE IIB                13                 71
  STAGE III                10                 19
  STAGE IIIA               15                 82
  STAGE IIIB                8                 64
  STAGE IIIC                7                 41
  STAGE IV                 12                 39
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17Q GAIN MUTATED      11  22  46  16
  17Q GAIN WILD-TYPE    42 104 234 108
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1               11                 42
  T2                  22                104
  T3                  46                234
  T4                  16                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
  17Q GAIN MUTATED    32  32  14  15
  17Q GAIN WILD-TYPE 168 150  82  82
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               32                168
  N1               32                150
  N2               14                 82
  N3               15                 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"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    78   9
  17Q GAIN WILD-TYPE 435  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     78    9
  17Q GAIN WILD-TYPE  435   30
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               78                435
  1                9                 30
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    20  81
  17Q GAIN WILD-TYPE 162 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     20   81
  17Q GAIN WILD-TYPE  162  346
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               20                162
  MALE                 81                346
[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                                                                  11
  17Q GAIN WILD-TYPE                                                                70
                    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)               11
  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)                 70
  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     1 100
  17Q GAIN WILD-TYPE   5 503
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1  100
  17Q GAIN WILD-TYPE    5  503
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 1                  5
  YES              100                503
[1] 2 2
[1] FALSE
D31V10, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    48   0   6   1
  17Q GAIN WILD-TYPE 299  18  13  24
D31V11, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               48                299
  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"
D31V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED      20                         7
  17Q GAIN WILD-TYPE   109                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    63
  17Q GAIN WILD-TYPE                                         1   322
D31V13, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                                   20                109
  BLACK OR AFRICAN AMERICAN                                7                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   63                322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  58
  17Q GAIN WILD-TYPE   7 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   58
  17Q GAIN WILD-TYPE    7  336
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               58                336
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    68  56
  18P GAIN WILD-TYPE 286 165
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               124                451 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                56                165 
$`18P GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A97I 
        7.63        13.94         4.21         0.53        12.82        12.16 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OM 
       60.39         3.68        25.41         4.31         8.94        47.93 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88Y 
       18.35         1.38         3.16         4.90         7.13         0.36 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37        13.41        27.12        83.24        46.09 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.76        12.59        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC 
       25.25         5.06        53.95        12.69        20.38         3.42 
TCGA-V5-A7RE TCGA-VR-A8EQ TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
        4.80        22.82        28.11        18.18        42.87        11.24 
TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6565 TCGA-BR-7722 
       15.91         2.10         6.97        18.35         9.17        15.32 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
        3.45        11.44         0.69         9.60         8.05        12.95 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8485 
        2.20        15.58         7.40        13.08         3.32         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD 
       20.22         1.12         8.22         0.72        13.51        20.65 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-A486 TCGA-CD-A4MH 
        1.15         2.83         3.25        13.15         3.42        12.20 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 
       21.99        22.98        12.03        11.93        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 
       15.22        12.79        14.66        13.78        11.31         2.96 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       15.65         7.40         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-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A663 
       13.08         6.44         6.74         5.56        60.56         9.86 
TCGA-R5-A7ZI TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
       61.25        35.61         0.92        21.73        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91U 
       17.85         1.87         9.27        11.93        18.74         1.71 
TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
        9.04        40.08        32.94         0.79 

$`18P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30        17.03         0.79        23.41         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        4.67        14.50       122.10        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF 
        6.28         3.16        30.25         0.30        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP 
        4.70        32.61        19.99        21.01         3.32         7.17 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       58.59        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        7.76         8.71        52.57        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.66        12.43         0.10        12.46        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HW 
       22.39         0.10        15.52        11.54        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.23        12.03        13.18         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        6.35         9.30        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.02         5.29        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       19.96        12.43         1.55        18.31         8.12        30.71 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN 
       46.19        15.06         9.17        10.16         3.42         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        9.44         6.61         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-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-7723 TCGA-BR-7851 
       23.93        15.42        28.01        18.15        28.73        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        9.07        12.76        18.71        17.49        14.43        12.26 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 
       20.55         0.56         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-A6RO TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39         5.36         5.19         1.41        12.59         6.51 
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-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       37.64         3.72        19.73        45.67        18.21         8.52 
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-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        16.87        19.04         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-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-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       46.26        16.31         2.50        12.79        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-A91V 
       36.69        11.70        61.22        20.81        22.68        36.16 
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-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-AA69 TCGA-VQ-AA6B 
       42.54        11.24        22.09        18.41        28.41        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 
       10.62 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               0.1                0.0 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             83.24             122.30 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             12.25              12.92 
[1] "0.1 - 83.2 (12.2)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         2        4       10        6        17        18
  18P GAIN WILD-TYPE       9       15       38       26        60        66
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED          10         19         10         15       12
  18P GAIN WILD-TYPE        19         78         62         33       39
                    vv
clus                 STAGE IVA
  18P GAIN MUTATED           1
  18P GAIN WILD-TYPE         3
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   2                  9
  STAGE IA                  4                 15
  STAGE IB                 10                 38
  STAGE II                  6                 26
  STAGE IIA                17                 60
  STAGE IIB                18                 66
  STAGE III                10                 19
  STAGE IIIA               19                 78
  STAGE IIIB               10                 62
  STAGE IIIC               15                 33
  STAGE IV                 12                 39
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18P GAIN MUTATED      14  23  61  28
  18P GAIN WILD-TYPE    39 103 219  96
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1               14                 39
  T2                  23                103
  T3                  61                219
  T4                  28                 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
  18P GAIN MUTATED    45  42  16  25
  18P GAIN WILD-TYPE 155 140  80  72
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               45                155
  N1               42                140
  N2               16                 80
  N3               25                 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"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   108   9
  18P GAIN WILD-TYPE 405  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    108    9
  18P GAIN WILD-TYPE  405   30
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0              108                405
  1                9                 30
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    40  94
  18P GAIN WILD-TYPE 142 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     40   94
  18P GAIN WILD-TYPE  142  333
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               40                142
  MALE                 94                333
[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                                                       33
  18P GAIN WILD-TYPE                                                    129
                    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)                          33
  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)                           129
  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     4 130
  18P GAIN WILD-TYPE   2 473
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4  130
  18P GAIN WILD-TYPE    2  473
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 4                  2
  YES              130                473
[1] 2 2
[1] FALSE
D32V10, continuous
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    65   5   4   5
  18P GAIN WILD-TYPE 282  13  15  20
D32V11, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               65                282
  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"
D32V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED      31                         1
  18P GAIN WILD-TYPE    98                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           0    84
  18P GAIN WILD-TYPE                                         1   301
D32V13, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                                   31                 98
  BLACK OR AFRICAN AMERICAN                                1                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   84                301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  82
  18P GAIN WILD-TYPE   5 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   82
  18P GAIN WILD-TYPE    5  312
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               82                312
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    40  33
  18Q GAIN WILD-TYPE 314 188
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                73                502 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                33                188 
$`18Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A625 
        7.63         5.92        13.94         4.21        33.27        12.82 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43E TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88Y 
       60.39         3.68        30.25         3.16         7.13         0.36 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49O TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HY 
        5.49        21.37        13.41         0.10        12.76        12.03 
TCGA-R6-A6KZ TCGA-S8-A6BW TCGA-VR-A8EQ TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
        5.06        20.38        22.82        18.18        42.87        11.24 
TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-BR-4184 TCGA-BR-6565 TCGA-BR-7901 TCGA-BR-8077 
       15.91         2.10         6.97         9.17         3.45         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        9.60         8.05        12.95         2.20        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8687 TCGA-BR-A4CS TCGA-BR-A4J1 
       13.08        25.18         1.12         8.22         1.48         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.51        20.65         1.15         2.83         3.25        13.15 
TCGA-CG-4460 TCGA-D7-5579 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-A4YY TCGA-D7-A6EX 
       21.99        11.93        15.22        12.79        13.78        11.31 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GD 
        0.56         5.52        26.47         5.92         0.76        22.75 
TCGA-HU-A4GF TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-R5-A7ZI 
       25.81        12.30        27.42        18.38        13.08        61.25 
TCGA-RD-A8N9 TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A91E TCGA-VQ-A91N 
       35.61         2.70         1.87         9.27        11.93        18.74 
TCGA-VQ-AA68 
       40.08 

$`18Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30        58.55         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69         6.21        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
       14.50        12.16       122.10        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       24.03         6.28         3.16         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
        0.10        13.15        15.35         0.10        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.00        12.23        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       29.59         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
        1.45        12.69         7.00        20.02         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        4.80        15.35         9.27         4.44        18.81        19.96 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN 
       46.19        15.06         9.17        10.16         3.42         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         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-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-8081 TCGA-BR-8285 TCGA-BR-8289 
       14.43        11.44        12.26        20.55         0.56         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-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        15.68        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-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-5801 TCGA-CD-5802 
       20.42        13.64        11.57         5.13        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-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-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-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 
       17.85        13.35        17.19        10.26        15.98        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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
        5.92        15.16        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-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-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         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-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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        23.84         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO 
        3.45        18.81         3.39         5.36         5.19         1.41 
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-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-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-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.50        12.79        17.85        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-A91U TCGA-VQ-A91V 
       11.70        61.22        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-AA69 
        2.66        42.54        11.24        22.09        18.41        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 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               0.1                0.0 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             61.25             122.30 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             11.93              12.82 
[1] "0.1 - 61.2 (11.9)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.5"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         3        2        5        5         6         9
  18Q GAIN WILD-TYPE       8       17       43       27        71        75
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           9         12          6         12        8
  18Q GAIN WILD-TYPE        20         85         66         36       43
                    vv
clus                 STAGE IVA
  18Q GAIN MUTATED           0
  18Q GAIN WILD-TYPE         4
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  2                 17
  STAGE IB                  5                 43
  STAGE II                  5                 27
  STAGE IIA                 6                 71
  STAGE IIB                 9                 75
  STAGE III                 9                 20
  STAGE IIIA               12                 85
  STAGE IIIB                6                 66
  STAGE IIIC               12                 36
  STAGE IV                  8                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18Q GAIN MUTATED       8  12  32  26
  18Q GAIN WILD-TYPE    45 114 248  98
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                8                 45
  T2                  12                114
  T3                  32                248
  T4                  26                 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
  18Q GAIN MUTATED    26  24  11  17
  18Q GAIN WILD-TYPE 174 158  85  80
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               26                174
  N1               24                158
  N2               11                 85
  N3               17                 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"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    68   5
  18Q GAIN WILD-TYPE 445  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     68    5
  18Q GAIN WILD-TYPE  445   34
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               68                445
  1                5                 34
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    27  54
  18Q GAIN WILD-TYPE 155 373
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     27   54
  18Q GAIN WILD-TYPE  155  373
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               27                155
  MALE                 54                373
[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                                                       22
  18Q GAIN WILD-TYPE                                                    140
                    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                                                 11
  18Q GAIN WILD-TYPE                                               67
                    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)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                11
  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)                           140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 75
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  67
  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  78
  18Q GAIN WILD-TYPE   3 525
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3   78
  18Q GAIN WILD-TYPE    3  525
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 3                  3
  YES               78                525
[1] 2 2
[1] FALSE
D33V10, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    42   4   3   3
  18Q GAIN WILD-TYPE 305  14  16  22
D33V11, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               42                305
  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"
D33V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED      18                         0
  18Q GAIN WILD-TYPE   111                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           0    51
  18Q GAIN WILD-TYPE                                         1   334
D33V13, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                                   18                111
  BLACK OR AFRICAN AMERICAN                                0                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   51                334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1  52
  18Q GAIN WILD-TYPE   6 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   52
  18Q GAIN WILD-TYPE    6  342
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               52                342
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    49  22
  19P GAIN WILD-TYPE 305 199
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                71                504 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                22                199 
$`19P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-IG-A3QL TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OO 
       58.55         8.94        20.09         3.16        24.00         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A8NG TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K 
        1.38         3.16        35.97        27.12        10.36         5.92 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-R6-A6XG 
       13.15         0.10        25.25        12.00         0.13        29.59 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EX TCGA-VR-AA7I TCGA-X8-AAAR 
       12.69        20.38        15.35        28.11        15.91        10.16 
TCGA-B7-A5TK TCGA-BR-6456 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8370 
        9.47        17.29        18.71        12.95        16.31         3.32 
TCGA-BR-A453 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8526 
        6.08        13.51        20.65        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-7916 
       18.54        15.22        21.14        16.44        16.24        14.07 
TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4H2 
        5.52        14.17        12.10        24.30        22.75        12.95 
TCGA-IN-7808 TCGA-IN-A6RP TCGA-R5-A7ZR TCGA-SW-A7EB TCGA-VQ-A8E3 TCGA-VQ-A8PE 
        3.45         6.44         6.08         5.79        21.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A91A TCGA-VQ-A91S TCGA-VQ-A925 TCGA-VQ-A92D 
       12.79        36.69        22.68         4.54        64.18 

$`19P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       16.24         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF 
        6.28        30.25         0.30         4.31         8.94         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L 
        8.71        13.41        83.24        52.57        46.09        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
       12.66        12.43        13.41         0.10        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        10.52        12.23        12.03        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       33.11         5.16         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         1.45         7.00        20.02         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80         9.27         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD 
       42.87        46.19        15.06        11.24         9.17         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.44         6.61         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-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        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-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.76        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-8295 
        9.60        20.55         8.05         0.56         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        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-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-A4CQ TCGA-BR-A4CS 
       10.68        12.56        13.87         7.53        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-A4PE 
        0.53        12.82         0.66        19.36         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-8527 TCGA-CD-8528 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 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-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        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-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-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-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-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       69.04        21.07         7.99        12.66        11.93        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        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-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-F1-6874 
        4.34         7.40         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX 
       17.06        59.54         5.03        13.58         0.56         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-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       11.41        10.62         0.76         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-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-A6RI 
        8.81        27.42        21.21        18.81         3.39        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-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-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-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-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87        19.04         0.92        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-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-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       20.81         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-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 

  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 
             13.64              12.59 
[1] "0.1 - 64.2 (13.6)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         1        1        5        3         9        11
  19P GAIN WILD-TYPE      10       18       43       29        68        73
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           5         15         11          5        6
  19P GAIN WILD-TYPE        24         82         61         43       45
                    vv
clus                 STAGE IVA
  19P GAIN MUTATED           1
  19P GAIN WILD-TYPE         3
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   1                 10
  STAGE IA                  1                 18
  STAGE IB                  5                 43
  STAGE II                  3                 29
  STAGE IIA                 9                 68
  STAGE IIB                11                 73
  STAGE III                 5                 24
  STAGE IIIA               15                 82
  STAGE IIIB               11                 61
  STAGE IIIC                5                 43
  STAGE IV                  6                 45
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19P GAIN MUTATED       5  19  40  11
  19P GAIN WILD-TYPE    48 107 240 113
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                5                 48
  T2                  19                107
  T3                  40                240
  T4                  11                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
  19P GAIN MUTATED    23  24  10  17
  19P GAIN WILD-TYPE 177 158  86  80
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               23                177
  N1               24                158
  N2               10                 86
  N3               17                 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"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    60   7
  19P GAIN WILD-TYPE 453  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     60    7
  19P GAIN WILD-TYPE  453   32
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               60                453
  1                7                 32
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    21  59
  19P GAIN WILD-TYPE 161 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     21   59
  19P GAIN WILD-TYPE  161  368
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               21                161
  MALE                 59                368
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19P GAIN MUTATED                                      12
  19P GAIN WILD-TYPE                                    59
                    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                                                 13
  19P GAIN WILD-TYPE                                               65
                    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                                           12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                13
  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                                             59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           145
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  65
  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  78
  19P GAIN WILD-TYPE   4 525
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   78
  19P GAIN WILD-TYPE    4  525
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 2                  4
  YES               78                525
[1] 2 2
[1] FALSE
D34V10, continuous
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    37   4   5   4
  19P GAIN WILD-TYPE 310  14  14  21
D34V11, 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"
D34V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED      19                         3
  19P GAIN WILD-TYPE   110                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           0    46
  19P GAIN WILD-TYPE                                         1   339
D34V13, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                                   19                110
  BLACK OR AFRICAN AMERICAN                                3                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   46                339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  52
  19P GAIN WILD-TYPE   6 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   52
  19P GAIN WILD-TYPE    6  342
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               52                342
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    66  38
  19Q GAIN WILD-TYPE 288 183
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               104                471 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                38                183 
$`19Q GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A4QS 
       58.55         7.63         8.94        16.24        20.09         3.88 
TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OQ 
        3.16        24.00         3.68        32.61         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV 
        3.16        35.97        13.55         5.49        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49U TCGA-LN-A4A6 TCGA-LN-A5U7 
       46.09        10.36         5.92        15.35         0.10        25.25 
TCGA-LN-A7HW TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8WG 
       12.00         0.13         5.06        14.70        29.59        12.69 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EX TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE 
       20.38        15.35        28.11        15.91        10.16         2.10 
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-BR-A4PD TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 
       13.51        20.65        13.18         0.07         0.07         0.16 
TCGA-CD-8535 TCGA-CD-A48C TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
        0.13        11.61        54.08        47.05        21.99        22.98 
TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6818 
        0.99         4.01        12.36        19.13        18.54        10.55 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8578 TCGA-D7-A4YU TCGA-EQ-8122 TCGA-EQ-A4SO 
       12.33        24.72        21.14        16.44         7.99        16.24 
TCGA-F1-6875 TCGA-FP-7916 TCGA-FP-A4BF TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       72.23        14.07         5.52        14.27        14.17        12.10 
TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-A6RL 
       24.30        22.75         2.10        12.95         3.45         5.19 
TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8N9 TCGA-SW-A7EB 
        6.44        60.56         6.08         8.61        35.61         5.79 
TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A91A 
       13.25        21.73         7.73        22.19        12.79        36.69 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T 
       22.68         1.71         2.01         4.54        64.18        11.24 
TCGA-VQ-AA6F TCGA-VQ-AA6K 
       54.12        12.43 

$`19Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       25.78        31.27        14.30         5.92        13.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69         6.21        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.50        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        4.31         8.94         4.70        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         7.17        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.95         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       13.41        83.24        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.10        13.15         0.10        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV 
       11.54        12.33        13.22         4.47        12.33        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.23        12.03        13.18        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         7.59         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.89         1.45         7.00        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42         4.80         9.27         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        42.87        46.19        15.06        11.24         9.17 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.44         6.61         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-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        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-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-8289 TCGA-BR-8295 TCGA-BR-8296 
       20.55         8.05         0.56         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        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-8371 
       17.52         0.95        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18        20.22        12.79        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-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        15.68         8.22        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-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-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-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 
        3.25        13.15         0.30         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-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-4443 
        1.02         7.99         8.05         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-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-D7-5578 TCGA-D7-5579 
       65.10        69.04        21.07         7.99        12.66        11.93 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8572 
       10.26        15.22        15.98        12.79        11.31        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-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-F1-6874 TCGA-F1-A448 
        4.34         7.40         7.13         0.62        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        19.53        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-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        1.51         5.92        12.59        11.41        10.62         0.76 
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-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-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.25        10.19         0.26        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        9.67         8.88         8.81        27.42        21.21        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-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-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-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       16.87        19.04         0.92        48.79         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       18.48        35.24        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.29        46.26        16.31         2.50         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-A91D TCGA-VQ-A91E 
       27.35        64.57        14.33        65.16        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        20.81        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        52.24         9.04        55.43         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        22.09        18.41        40.08 
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-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        10.62         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 
             12.87              12.76 
[1] "0.1 - 72.2 (12.9)"  "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         2        3        8        5        11        15
  19Q GAIN WILD-TYPE       9       16       40       27        66        69
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           7         22         14          8        8
  19Q GAIN WILD-TYPE        22         75         58         40       43
                    vv
clus                 STAGE IVA
  19Q GAIN MUTATED           2
  19Q GAIN WILD-TYPE         2
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   2                  9
  STAGE IA                  3                 16
  STAGE IB                  8                 40
  STAGE II                  5                 27
  STAGE IIA                11                 66
  STAGE IIB                15                 69
  STAGE III                 7                 22
  STAGE IIIA               22                 75
  STAGE IIIB               14                 58
  STAGE IIIC                8                 40
  STAGE IV                  8                 43
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19Q GAIN MUTATED       9  24  58  16
  19Q GAIN WILD-TYPE    44 102 222 108
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                9                 44
  T2                  24                102
  T3                  58                222
  T4                  16                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
  19Q GAIN MUTATED    31  38  13  24
  19Q GAIN WILD-TYPE 169 144  83  73
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               31                169
  N1               38                144
  N2               13                 83
  N3               24                 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"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    89   8
  19Q GAIN WILD-TYPE 424  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     89    8
  19Q GAIN WILD-TYPE  424   31
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               89                424
  1                8                 31
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    28  86
  19Q GAIN WILD-TYPE 154 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     28   86
  19Q GAIN WILD-TYPE  154  341
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               28                154
  MALE                 86                341
[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                                                       24
  19Q GAIN WILD-TYPE                                                    138
                    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)                          24
  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)                           138
  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     4 110
  19Q GAIN WILD-TYPE   2 493
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4  110
  19Q GAIN WILD-TYPE    2  493
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 4                  2
  YES              110                493
[1] 2 2
[1] FALSE
D35V10, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    55   6   6   4
  19Q GAIN WILD-TYPE 292  12  13  21
D35V11, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               55                292
  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"
D35V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED      25                         4
  19Q GAIN WILD-TYPE   104                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           1    67
  19Q GAIN WILD-TYPE                                         0   318
D35V13, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                                   25                104
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   67                318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  69
  19Q GAIN WILD-TYPE   6 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   69
  19Q GAIN WILD-TYPE    6  325
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               69                325
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   195 132
  20P GAIN WILD-TYPE 159  89
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               327                248 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               132                 89 
$`20P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        20.09         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
        2.63        20.12         3.88         0.53        17.03        23.41 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A939 
        4.67        14.50        12.16       122.10         3.68        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        25.22         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        4.31        24.00         4.70        47.93        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         0.36         7.40        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       12.92        16.47         5.49         8.71        13.41        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S 
       52.57        46.09        10.36        10.45         0.10        13.15 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 
        0.10        12.49        12.76         0.10        11.54        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ 
       25.25        12.23        13.18         0.13         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        14.70         7.04         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.89        12.69        20.02         5.29         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
        9.27         4.44        19.96         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        42.87        46.19        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TJ 
       15.91         3.42         2.10         2.66        19.73        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
        9.47         9.44         6.61         6.97         4.64        18.35 
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
       30.90         6.61        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-7196 
       39.12         9.17        18.05        19.89        21.11        12.82 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        35.24        15.42        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
        3.45        12.76        18.71        11.44         0.69         9.60 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 
        0.56        16.31         2.20        15.58         7.40        14.04 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       14.79         0.26         5.39        25.18         9.21        20.22 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 
       15.81         9.34         7.53         0.49        11.54         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-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
        1.48         0.72         0.53        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 
        1.15        13.64         3.25        13.15        13.18         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-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.10         0.13         0.13         3.42         9.34        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4304 
       11.61         6.58        12.20         0.10        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
       15.95         7.99        54.08         4.01        14.01        47.05 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5718 
       12.03        18.97         7.07        12.00        30.97        36.00 
TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        1.02         0.99        12.03        28.96        79.07         4.01 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 
        7.99        12.36        12.66        11.93        19.13        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 
       13.35        17.19        10.26        15.22        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       12.33        24.72        19.50        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
        5.92        15.16        13.71        11.24        11.31         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6874 
        2.96        15.65         8.38         7.40         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23        11.38        19.53        14.07        22.29        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        0.56         5.52         0.23        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       14.27        12.59        10.62         0.76        24.30        12.30 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL 
        9.67        27.42        21.21         3.45        18.38         5.19 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 
        6.74        12.59         5.56         1.81        13.51         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       60.56        20.15        37.64         9.86        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 
       61.25         6.08         9.24         8.61        16.67       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       57.44         8.94        35.61         5.79        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       35.24        21.73        46.26        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        2.70        17.85        15.65        27.35        64.57        65.16 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       11.93        18.74        22.68         1.71         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       52.24         9.04         2.01         5.72        64.18        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G 
       42.54        11.24        18.41        32.94        29.98        26.04 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        10.62         0.79 

$`20P GAIN WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A4P3 
       14.30        58.55         7.63         6.21        20.78        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA 
        9.30         0.79        12.82         9.96        14.86        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93F 
       60.39        68.02        41.52        42.77        25.41        24.03 
TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        6.28         8.94         3.68        32.61        19.99        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 
        3.32         7.17         3.16         8.71        25.12         3.95 
TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        13.48        13.55        13.22         7.76        21.37 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U 
       83.24         5.92        12.66        12.43        13.41        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        13.25        12.46        12.59        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW 
       15.52        12.33        13.22         4.47        10.52        12.00 
TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6XG TCGA-R6-A6Y0 
       12.03        33.11         5.16         7.82        29.59        53.95 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EQ 
        1.45         7.00        20.38        15.35        18.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-AA4G TCGA-X8-AAAR TCGA-B7-5816 TCGA-B7-5818 
       12.43        18.31        15.06        10.16        26.70        11.70 
TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6456 
       19.56         7.43         6.18         9.57        34.68        17.29 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       26.10        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-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
        9.07        17.49        14.43        12.26        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       12.95         2.66         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-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 
       11.80        19.17        15.85         3.72         1.12        12.79 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 
       13.45         6.28        15.81        16.44        12.56         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
       13.41        13.51        12.89         8.98        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.66        19.36        20.65        11.57         5.13         2.83 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MJ 
        0.30         0.07         0.10         0.10        11.31        12.62 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 
        3.02         1.02         8.05        29.98        19.07        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
        0.00         9.01        22.98         6.97         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-6519 
      105.07        15.02        65.10        69.04        21.07        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8572 
       18.84        18.61        17.85        15.98        12.79        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YY TCGA-D7-A4Z0 
       17.19        18.21        14.66        21.14        13.78        14.76 
TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-A448 
       11.44         4.34         7.13         0.62        16.24        21.27 
TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8249 
        3.48        59.54         5.03        13.58        18.08        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
       11.41        12.10         5.59        11.84        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.98         6.51        19.36        12.30         8.88         8.81 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.81         3.39         5.36        13.08         1.41         6.44 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
        6.51         7.82         2.53         3.72        19.73        45.67 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        4.60        11.05         5.13       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT 
      116.38        71.38        16.87        19.04         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        5.46        18.48        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-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       13.35        26.24        14.33        36.69        11.70        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       20.81        36.16         9.50        55.43         4.54         6.58 
TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F 
        2.66        22.09        40.08        28.41        17.13        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J 
       16.14        21.11 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.00 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             122.1              122.3 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            12.160             13.465 
[1] "0.1 - 122.1 (12.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         4       10       23       17        41        45
  20P GAIN WILD-TYPE       7        9       25       15        36        39
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED          17         63         39         28       24
  20P GAIN WILD-TYPE        12         34         33         20       27
                    vv
clus                 STAGE IVA
  20P GAIN MUTATED           4
  20P GAIN WILD-TYPE         0
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   4                  7
  STAGE IA                 10                  9
  STAGE IB                 23                 25
  STAGE II                 17                 15
  STAGE IIA                41                 36
  STAGE IIB                45                 39
  STAGE III                17                 12
  STAGE IIIA               63                 34
  STAGE IIIB               39                 33
  STAGE IIIC               28                 20
  STAGE IV                 24                 27
  STAGE IVA                 4                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20P GAIN MUTATED      28  65 166  62
  20P GAIN WILD-TYPE    25  61 114  62
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               28                 25
  T2                  65                 61
  T3                 166                114
  T4                  62                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P GAIN MUTATED    99 112  52  52
  20P GAIN WILD-TYPE 101  70  44  45
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               99                101
  N1              112                 70
  N2               52                 44
  N3               52                 45
[1] 4 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   284  20
  20P GAIN WILD-TYPE 229  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    284   20
  20P GAIN WILD-TYPE  229   19
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              284                229
  1               20                 19
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    87 253
  20P GAIN WILD-TYPE  95 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     87  253
  20P GAIN WILD-TYPE   95  174
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               87                 95
  MALE                253                174
[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                                                                  51
  20P GAIN WILD-TYPE                                                                30
                    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                                                          9
  20P GAIN WILD-TYPE                                                       12
                    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)               51
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         9
  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)                 30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          12
  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     2 338
  20P GAIN WILD-TYPE   4 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  338
  20P GAIN WILD-TYPE    4  265
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 2                  4
  YES              338                265
[1] 2 2
[1] FALSE
D36V10, continuous
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED   189   9   9  14
  20P GAIN WILD-TYPE 158   9  10  11
D36V11, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              189                158
  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"
D36V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED      72                         7
  20P GAIN WILD-TYPE    57                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           1   216
  20P GAIN WILD-TYPE                                         0   169
D36V13, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                                   72                 57
  BLACK OR AFRICAN AMERICAN                                7                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  216                169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     5 221
  20P GAIN WILD-TYPE   2 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5  221
  20P GAIN WILD-TYPE    2  173
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  2
  NOT HISPANIC OR LATINO              221                173
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   221 148
  20Q GAIN WILD-TYPE 133  73
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               369                206 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               148                 73 
$`20Q GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85         2.63        20.12         3.88         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE 
       23.41         4.67        14.50        12.16       122.10         3.68 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        31.56        25.22         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31        24.00         3.68         4.70        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         7.40        55.50         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R 
       27.12        52.57        46.09        10.36        10.45         0.10 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.15         0.10         0.10        12.49        12.76         0.10 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       12.33        25.25        12.23        12.03        13.18         0.13 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.02         5.29         3.42         4.80         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
        4.44        19.96         1.55         8.12        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-Z6-A8JE 
       42.87        46.19        11.24         9.17         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        2.66        19.73        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6453 
        6.97         4.64        18.35        30.90         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 
        9.17        18.05        19.89        21.11        12.82         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.24        15.42        18.15        15.32        28.73         3.45 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       12.76        18.71        14.43        11.44         0.69         9.60 
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-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-8590 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       20.22         9.34         7.53         0.49        11.54        16.44 
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-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 
       22.26         1.48        12.89         0.72         0.53        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
        0.46        20.65        20.42         1.15        13.64         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
        0.10        20.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 
       54.08         4.01        14.01        47.05        12.03        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        22.98        30.97        36.00         1.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        28.96        79.07         4.01        69.04 
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-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.54        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6818 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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
        5.92        15.16        13.71        11.24        11.31         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-8122 TCGA-EQ-A4SO 
        2.96        15.65         8.38         7.40         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 
       22.29        17.06         0.56         5.52         0.23        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        1.51         5.92        14.27        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD 
       10.62         0.76        24.30        12.30         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        11.77         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       27.42        21.21         3.45         3.39        18.38         5.19 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
        6.74        12.59         5.56         1.81        13.51         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-RD-A7BT TCGA-RD-A7C1 
       18.21         8.52        61.25         6.08         8.61        16.67 
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-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-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       46.26        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PQ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        18.74        22.68         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 
        9.50         9.73        52.24         9.04         2.01         4.54 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        64.18        21.04        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       40.08        32.94        29.98        54.12        26.04        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        10.62         0.79 

$`20Q GAIN WILD-TYPE`
TCGA-2H-A9GL TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT 
        5.92         6.21        20.09        20.78        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB 
        0.79        12.82         9.96        14.86        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC 
       68.02        41.52        42.77        25.41        24.03         6.28 
TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A88T TCGA-L5-A88W 
        8.94        19.99        21.01         7.17         8.71        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NU 
        3.95         3.02        13.48        13.55         7.76        83.24 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49W 
        5.92        12.66        12.43        13.41        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.46        12.59        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-M9-A5M8 
       12.33        13.22         4.47        10.52        12.00        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO 
        5.16         7.82         1.45        20.38        15.35        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I 
       22.82        12.43        18.31        30.71        15.06        15.91 
TCGA-X8-AAAR TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4267 
       10.16        26.70        11.70        19.56         7.43         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 
        9.57        34.68        32.78        25.61        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       30.90        31.20        32.94        24.76        23.93        28.01 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       12.43         9.07        17.49        12.26        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       12.95         6.18        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-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       19.17        15.85         3.72         1.12        12.79        15.81 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       13.45         6.28        15.81        12.56         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
       13.51         8.98        14.17        12.82         0.66        19.36 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8531 
       11.57         5.13         2.83         0.30         0.07         0.10 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4443 
        0.10        11.31        12.62         3.02         1.02        29.98 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 
       19.07        21.99         0.00         9.01         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6522 
        6.02       105.07        15.02        65.10        21.07        18.61 
TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-A4YY TCGA-D7-A4Z0 
       17.85        12.79        17.19        18.21        13.78        14.76 
TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-8209 
       11.44         4.34         7.13         0.62        21.27        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G3 TCGA-HU-A4G8 
        5.03        13.58        18.08        11.41         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 
       24.20        21.37        29.98         6.51        19.36         8.88 
TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
        8.81        18.81         5.36        13.08         1.41         6.44 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 
        6.51         7.82         3.72        19.73         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         5.13       122.30        40.64       116.38        71.38 
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-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-A91D TCGA-VQ-A91K 
        9.27        23.41        13.35        26.24        11.70        61.22 
TCGA-VQ-A91Q TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA69 
       20.81        55.43         6.58         2.66        22.09        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6I 
       17.13        16.14 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.00 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             122.1              122.3 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            12.430             13.235 
[1] "0.1 - 122.1 (12.4)" "0.0 - 122.3 (13.2)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         7       11       27       18        43        55
  20Q GAIN WILD-TYPE       4        8       21       14        34        29
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED          20         71         46         30       28
  20Q GAIN WILD-TYPE         9         26         26         18       23
                    vv
clus                 STAGE IVA
  20Q GAIN MUTATED           4
  20Q GAIN WILD-TYPE         0
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   7                  4
  STAGE IA                 11                  8
  STAGE IB                 27                 21
  STAGE II                 18                 14
  STAGE IIA                43                 34
  STAGE IIB                55                 29
  STAGE III                20                  9
  STAGE IIIA               71                 26
  STAGE IIIB               46                 26
  STAGE IIIC               30                 18
  STAGE IV                 28                 23
  STAGE IVA                 4                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20Q GAIN MUTATED      34  77 187  68
  20Q GAIN WILD-TYPE    19  49  93  56
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               34                 19
  T2                  77                 49
  T3                 187                 93
  T4                  68                 56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q GAIN MUTATED   110 125  66  59
  20Q GAIN WILD-TYPE  90  57  30  38
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              110                 90
  N1              125                 57
  N2               66                 30
  N3               59                 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   321  22
  20Q GAIN WILD-TYPE 192  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    321   22
  20Q GAIN WILD-TYPE  192   17
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              321                192
  1               22                 17
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    98 289
  20Q GAIN WILD-TYPE  84 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     98  289
  20Q GAIN WILD-TYPE   84  138
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               98                 84
  MALE                289                138
[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                                                       95
  20Q GAIN WILD-TYPE                                                     67
                    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                                                         12
  20Q GAIN WILD-TYPE                                                        9
                    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)                          95
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        12
  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)                            67
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                           9
  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     4 383
  20Q GAIN WILD-TYPE   2 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4  383
  20Q GAIN WILD-TYPE    2  220
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 4                  2
  YES              383                220
[1] 2 2
[1] FALSE
D37V10, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   225  10  10  14
  20Q GAIN WILD-TYPE 122   8   9  11
D37V11, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              225                122
  R1               10                  8
  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"
D37V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED      79                        10
  20Q GAIN WILD-TYPE    50                         3
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           1   244
  20Q GAIN WILD-TYPE                                         0   141
D37V13, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                                   79                 50
  BLACK OR AFRICAN AMERICAN                               10                  3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  244                141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     6 245
  20Q GAIN WILD-TYPE   1 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6  245
  20Q GAIN WILD-TYPE    1  149
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  1
  NOT HISPANIC OR LATINO              245                149
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    23   9
  21Q GAIN WILD-TYPE 331 212
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                32                543 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 9                212 
$`21Q GAIN MUTATED`
TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-L5-A8NE TCGA-L5-A8NN 
        2.63        23.41         4.67        14.50        55.50         5.49 
TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 TCGA-S8-A6BV TCGA-VR-A8EP 
       10.45        15.35         0.10        12.59        20.02        19.96 
TCGA-X8-AAAR TCGA-BR-6456 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8295 
       10.16        17.29         3.45         0.69        12.95         2.20 
TCGA-BR-8486 TCGA-BR-8687 TCGA-BR-A44U TCGA-CD-5799 TCGA-CD-A486 TCGA-D7-6527 
       20.22         8.22        13.87         3.25         3.42        10.26 
TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A6F0 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GH 
       15.22        12.33         2.96         5.92        22.75        11.77 
TCGA-HU-A4HD TCGA-IN-A6RP 
       27.42         6.44 

$`21Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        6.21        33.27        20.09         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82         9.96        14.86        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        3.16        30.25         0.30         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.68         4.70        32.61        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       83.24        52.57        46.09        10.36         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X 
       12.43        13.41         0.10        13.15        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         1.45        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.06        11.24         9.17        15.91         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-8060 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43        11.44        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
       20.55         8.05         0.56         2.66        16.31        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-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-8690 TCGA-BR-A44T 
       15.81        16.44         9.86        15.68        10.68        12.56 
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-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-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-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-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-D7-6521 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-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        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-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-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-HJ-7597 
       13.58         0.56         5.52         0.23        18.08        26.47 
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-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        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-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-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-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-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-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-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-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 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               0.1                0.0 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              55.5              122.3 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             11.11              12.79 
[1] "0.1 - 55.5 (11.1)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         0        2        3        3         7         6
  21Q GAIN WILD-TYPE      11       17       45       29        70        78
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           1          3          4          3        1
  21Q GAIN WILD-TYPE        28         94         68         45       50
                    vv
clus                 STAGE IVA
  21Q GAIN MUTATED           0
  21Q GAIN WILD-TYPE         4
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                 11
  STAGE IA                  2                 17
  STAGE IB                  3                 45
  STAGE II                  3                 29
  STAGE IIA                 7                 70
  STAGE IIB                 6                 78
  STAGE III                 1                 28
  STAGE IIIA                3                 94
  STAGE IIIB                4                 68
  STAGE IIIC                3                 45
  STAGE IV                  1                 50
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  21Q GAIN MUTATED       4   7  18   5
  21Q GAIN WILD-TYPE    49 119 262 119
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                4                 49
  T2                   7                119
  T3                  18                262
  T4                   5                119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q GAIN MUTATED    14  11   5   3
  21Q GAIN WILD-TYPE 186 171  91  94
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               14                186
  N1               11                171
  N2                5                 91
  N3                3                 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"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    31   1
  21Q GAIN WILD-TYPE 482  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     31    1
  21Q GAIN WILD-TYPE  482   38
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               31                482
  1                1                 38
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     9  25
  21Q GAIN WILD-TYPE 173 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9   25
  21Q GAIN WILD-TYPE  173  402
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                9                173
  MALE                 25                402
[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  34
  21Q GAIN WILD-TYPE   6 569
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   34
  21Q GAIN WILD-TYPE    6  569
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  6
  YES               34                569
[1] 2 2
[1] FALSE
D38V10, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    17   1   1   0
  21Q GAIN WILD-TYPE 330  17  18  25
D38V11, 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"
D38V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED      12                         0
  21Q GAIN WILD-TYPE   117                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           0    21
  21Q GAIN WILD-TYPE                                         1   364
D38V13, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                                   12                117
  BLACK OR AFRICAN AMERICAN                                0                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   21                364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  30
  21Q GAIN WILD-TYPE   7 364
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   30
  21Q GAIN WILD-TYPE    7  364
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               30                364
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    39  21
  22Q GAIN WILD-TYPE 315 200
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                60                515 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                21                200 
$`22Q GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A97H TCGA-L5-A43E TCGA-L5-A43J 
       20.09         0.85        20.78        14.50        30.25         4.31 
TCGA-L5-A4OM TCGA-L5-A8NT TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 
       47.93        27.12        12.59        12.49        12.59         0.10 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        12.33        13.22        12.33        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC 
       12.23         0.13         5.16        12.69        20.38         3.42 
TCGA-VR-A8EP TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-B7-5818 
       19.96         8.12        28.11        18.18        11.24        11.70 
TCGA-BR-4187 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8486 TCGA-BR-A452 
        4.64        35.24        28.73        18.71        20.22         7.53 
TCGA-BR-A4J8 TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 TCGA-CG-4436 TCGA-D7-6521 
       13.51         3.25         0.07         0.10         7.99        18.54 
TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4Z0 TCGA-D7-A6F0 TCGA-F1-6875 TCGA-FP-7998 
       15.98        14.66        14.76         2.96        72.23        22.29 
TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-A6RO 
       12.10        11.77         6.25        12.30         3.45         1.41 
TCGA-KB-A6F7 TCGA-RD-A8N6 TCGA-VQ-A8PJ TCGA-VQ-A91D TCGA-VQ-AA68 TCGA-VQ-AA6K 
       60.56         8.94         2.70        11.70        40.08        12.43 

$`22Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        6.21        33.27         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         0.30         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A5U5 
        0.10        12.46        12.76        22.39        15.52         4.47 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       10.52        12.03        13.18        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.02         5.29         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
       18.81        22.82        12.43         1.55        18.31        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       42.87        46.19        15.06         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI 
        3.42         2.10         2.66        19.73        26.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-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-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-8487 
       15.85         3.72         5.39        25.18         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-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-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        2.83        13.15        13.18         0.30         0.07         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-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-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-D7-6817 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-D7-8578 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-A6ET 
       14.27        16.44         5.92        15.16        13.78        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-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-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-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-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        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-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
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-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-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        9.67         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38         5.36         5.19        13.08         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-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-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-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-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-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       36.69        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-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        21.11        10.62         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 
             12.38              12.82 
[1] "0.1 - 72.2 (12.4)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         1        5        6        3        12         7
  22Q GAIN WILD-TYPE      10       14       42       29        65        77
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           3          8          6          5        2
  22Q GAIN WILD-TYPE        26         89         66         43       49
                    vv
clus                 STAGE IVA
  22Q GAIN MUTATED           1
  22Q GAIN WILD-TYPE         3
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                 10
  STAGE IA                  5                 14
  STAGE IB                  6                 42
  STAGE II                  3                 29
  STAGE IIA                12                 65
  STAGE IIB                 7                 77
  STAGE III                 3                 26
  STAGE IIIA                8                 89
  STAGE IIIB                6                 66
  STAGE IIIC                5                 43
  STAGE IV                  2                 49
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  22Q GAIN MUTATED       7  19  23  10
  22Q GAIN WILD-TYPE    46 107 257 114
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1                7                 46
  T2                  19                107
  T3                  23                257
  T4                  10                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
  22Q GAIN MUTATED    30  10   9   9
  22Q GAIN WILD-TYPE 170 172  87  88
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               30                170
  N1               10                172
  N2                9                 87
  N3                9                 88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    52   4
  22Q GAIN WILD-TYPE 461  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     52    4
  22Q GAIN WILD-TYPE  461   35
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               52                461
  1                4                 35
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    16  46
  22Q GAIN WILD-TYPE 166 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     16   46
  22Q GAIN WILD-TYPE  166  381
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               16                166
  MALE                 46                381
[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  62
  22Q GAIN WILD-TYPE   6 541
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   62
  22Q GAIN WILD-TYPE    6  541
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  6
  YES               62                541
[1] 2 2
[1] FALSE
D39V10, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    27   1   1   1
  22Q GAIN WILD-TYPE 320  17  18  24
D39V11, 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"
D39V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED      24                         2
  22Q GAIN WILD-TYPE   105                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    32
  22Q GAIN WILD-TYPE                                         1   353
D39V13, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                                   24                105
  BLACK OR AFRICAN AMERICAN                                2                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   32                353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     2  45
  22Q GAIN WILD-TYPE   5 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   45
  22Q GAIN WILD-TYPE    5  349
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               45                349
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    34  30
  XP GAIN WILD-TYPE 320 191
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               64               511 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               30               191 
$`XP GAIN MUTATED`
TCGA-IG-A51D TCGA-JY-A6F8 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OQ TCGA-L5-A4OR 
       17.03       122.10         4.31        19.99         1.38         3.16 
TCGA-L5-A88Y TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A2 
        0.36         5.49        21.37        13.15         0.10        12.49 
TCGA-LN-A4A4 TCGA-LN-A7HZ TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EY 
       12.59        13.18         2.89         3.42        15.35        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-BR-4187 TCGA-BR-6801 TCGA-BR-7197 
       18.18        46.19        19.73         4.64        21.11         9.21 
TCGA-BR-7717 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8365 TCGA-BR-8678 TCGA-BR-A452 
       18.15        17.49         0.69        17.52        11.54         7.53 
TCGA-BR-A4CS TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-4436 TCGA-CG-4460 
        1.48         0.10         9.34         6.58         7.99        21.99 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5726 TCGA-CG-5727 TCGA-D7-6519 TCGA-D7-8576 
       12.00        36.00        28.96        79.07        20.55        14.66 
TCGA-D7-A6EV TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-HU-8244 
       11.24         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-A7BT TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8PY 
       18.21         8.61         8.94        48.79        18.48        14.33 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.93        20.81        22.68         1.71 

$`XP GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       24.03         6.28         3.16        30.25         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       24.00         3.68         4.70        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         7.17        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
        0.10        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.23        12.03         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.02        20.38         5.29         4.80         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        4.44        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       18.31         8.12        28.11        42.87        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91        10.16         3.42         2.10         2.66 
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-8059 TCGA-BR-8060 TCGA-BR-8078 
        9.07        12.76        18.71        14.43        11.44        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-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-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-A453 TCGA-BR-A4CQ 
        8.22        10.68        12.56        13.87         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-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-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        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-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-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-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-D7-8578 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-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-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-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
        5.59        11.84         3.25        22.75        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.25        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-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-A7ZF TCGA-R5-A7ZI 
        3.72        19.73         9.86        45.67         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-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.25        13.02        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-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-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       18.74        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 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
              0.1               0.0 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            122.1             122.3 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           13.165            12.760 
[1] "0.1 - 122.1 (13.2)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         2        6        5        3        11         7
  XP GAIN WILD-TYPE       9       13       43       29        66        77
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           2          8          8          4        8
  XP GAIN WILD-TYPE        27         89         64         44       43
                   vv
clus                STAGE IVA
  XP GAIN MUTATED           0
  XP GAIN WILD-TYPE         4
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  2                 9
  STAGE IA                 6                13
  STAGE IB                 5                43
  STAGE II                 3                29
  STAGE IIA               11                66
  STAGE IIB                7                77
  STAGE III                2                27
  STAGE IIIA               8                89
  STAGE IIIB               8                64
  STAGE IIIC               4                44
  STAGE IV                 8                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XP GAIN MUTATED      10  14  30  12
  XP GAIN WILD-TYPE    43 112 250 112
D40V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1              10                43
  T2                 14               112
  T3                 30               250
  T4                 12               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
  XP GAIN MUTATED    30  16   9  10
  XP GAIN WILD-TYPE 170 166  87  87
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              30               170
  N1              16               166
  N2               9                87
  N3              10                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"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    56   2
  XP GAIN WILD-TYPE 457  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     56    2
  XP GAIN WILD-TYPE  457   37
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              56               457
  1               2                37
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    23  46
  XP GAIN WILD-TYPE 159 381
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     23   46
  XP GAIN WILD-TYPE  159  381
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              23               159
  MALE                46               381
[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                                                       16
  XP GAIN WILD-TYPE                                                    146
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XP GAIN MUTATED                                                                  13
  XP GAIN WILD-TYPE                                                                68
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XP GAIN MUTATED                                                 12
  XP GAIN WILD-TYPE                                               66
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  XP GAIN MUTATED                                                          1
  XP GAIN WILD-TYPE                                                       20
                   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)                         16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  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)                          146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 66
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  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     1  68
  XP GAIN WILD-TYPE   5 535
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1   68
  XP GAIN WILD-TYPE    5  535
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                1                 5
  YES              68               535
[1] 2 2
[1] FALSE
D40V10, continuous
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    38   1   3   3
  XP GAIN WILD-TYPE 309  17  16  22
D40V11, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              38               309
  R1               1                17
  R2               3                16
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XP GAIN MUTATED      17                         6
  XP GAIN WILD-TYPE   112                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP GAIN MUTATED                                           1    35
  XP GAIN WILD-TYPE                                         0   350
D40V13, multiclass
                                           clus
vv                                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                                  17               112
  BLACK OR AFRICAN AMERICAN                               6                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  35               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0  43
  XP GAIN WILD-TYPE   7 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   43
  XP GAIN WILD-TYPE    7  351
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              43               351
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    45  36
  XQ GAIN WILD-TYPE 309 185
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               81               494 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               36               185 
$`XQ GAIN MUTATED`
TCGA-2H-A9GI TCGA-IG-A3QL TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       14.30        20.09         3.88         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A43J 
        9.96         4.67       122.10        44.75        23.18         4.31 
TCGA-L5-A4OI TCGA-L5-A4OQ TCGA-L5-A88Y TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49K 
       19.99         1.38         0.36         5.49        21.37         5.92 
TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A7HZ 
       12.66         0.10         0.10        12.49        12.59        13.18 
TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ 
        2.89        20.02        15.35        18.31        30.71        18.18 
TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-BR-4187 TCGA-BR-6458 TCGA-BR-6801 TCGA-BR-7717 
       46.19        19.73         4.64        19.33        21.11        18.15 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8683 TCGA-BR-A452 
       17.49         0.69        13.08        17.52         9.86         7.53 
TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 
        0.10         9.34         6.58        21.99        12.00        36.00 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5734 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       28.96        79.07         7.99        17.19        15.22        15.98 
TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 
       11.24        15.65         0.62         7.99        72.23         3.48 
TCGA-HU-8244 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
       14.27        24.30        12.30        24.20        22.75        25.81 
TCGA-HU-A4GT TCGA-HU-A4HD TCGA-IN-7808 TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A8N6 
        6.51        27.42         3.45        45.67         8.61         8.94 
TCGA-VQ-A8DT TCGA-VQ-A8PC TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91S TCGA-VQ-A91U 
       48.79        46.26        14.33        11.93        22.68         1.71 
TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 
       52.24        64.18        40.08 

$`XQ GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        9.30         0.79        12.82        14.86        14.50        12.16 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        6.94         8.71         2.60        25.12         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22         7.76         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       27.12        83.24        52.57        46.09        10.36        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41         0.10        13.15        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.59        12.76        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.00        12.23        12.03         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        1.45        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80         9.27         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G 
       12.43         1.55         8.12        28.11        42.87        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        10.16         3.42         2.10 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         6.97         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-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        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-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-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        15.42        28.01        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        12.76        18.71        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-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-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50         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-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-8686 
        7.53         0.49        11.54        15.81        16.44        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-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-8529 
        0.07         0.07         0.07         0.07         0.07         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-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        3.42        11.31        12.43        11.61        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-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04        21.07        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-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        10.26        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-A4SO 
        2.96         8.38         4.34         7.40         7.13        16.24 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 
        0.23        18.08        26.47         1.51         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       14.17        11.41        12.10        10.62         0.76         5.59 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       11.84         3.25        11.77        21.37        29.98         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-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-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-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-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-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-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-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92         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-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        28.96        34.29        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-A8PZ 
       15.65        13.35        26.24        27.35        64.57        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V 
       36.69        11.70        61.22        18.74        20.81        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-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        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-VQ-AA6K 
       17.13        54.12        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              0.1               0.0 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            122.1             122.3 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            15.22             12.59 
[1] "0.1 - 122.1 (15.2)" "0.0 - 122.3 (12.6)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         2        5        6        2        14        15
  XQ GAIN WILD-TYPE       9       14       42       30        63        69
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           4         12         10          5        8
  XQ GAIN WILD-TYPE        25         85         62         43       43
                   vv
clus                STAGE IVA
  XQ GAIN MUTATED           0
  XQ GAIN WILD-TYPE         4
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  2                 9
  STAGE IA                 5                14
  STAGE IB                 6                42
  STAGE II                 2                30
  STAGE IIA               14                63
  STAGE IIB               15                69
  STAGE III                4                25
  STAGE IIIA              12                85
  STAGE IIIB              10                62
  STAGE IIIC               5                43
  STAGE IV                 8                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XQ GAIN MUTATED      10  18  43  14
  XQ GAIN WILD-TYPE    43 108 237 110
D41V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1              10                43
  T2                 18               108
  T3                 43               237
  T4                 14               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
  XQ GAIN MUTATED    34  28  13   9
  XQ GAIN WILD-TYPE 166 154  83  88
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              34               166
  N1              28               154
  N2              13                83
  N3               9                88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    72   5
  XQ GAIN WILD-TYPE 441  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     72    5
  XQ GAIN WILD-TYPE  441   34
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              72               441
  1               5                34
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    26  61
  XQ GAIN WILD-TYPE 156 366
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     26   61
  XQ GAIN WILD-TYPE  156  366
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              26               156
  MALE                61               366
[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                                                       15
  XQ GAIN WILD-TYPE                                                    147
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                                  12
  XQ GAIN WILD-TYPE                                                                69
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XQ GAIN MUTATED                                                 19
  XQ GAIN WILD-TYPE                                               59
                   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)                         15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               19
  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)                          147
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 59
  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  87
  XQ GAIN WILD-TYPE   6 516
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   87
  XQ GAIN WILD-TYPE    6  516
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                 6
  YES              87               516
[1] 2 2
[1] FALSE
D41V10, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    43   0   3   3
  XQ GAIN WILD-TYPE 304  18  16  22
D41V11, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              43               304
  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"
D41V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED      27                         4
  XQ GAIN WILD-TYPE   102                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           1    46
  XQ GAIN WILD-TYPE                                         0   339
D41V13, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                                  27               102
  BLACK OR AFRICAN AMERICAN                               4                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  46               339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  56
  XQ GAIN WILD-TYPE   6 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   56
  XQ GAIN WILD-TYPE    6  338
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              56               338
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    54  37
  1P LOSS WILD-TYPE 300 184
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               91               484 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               37               184 
$`1P LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-JY-A6FB 
       14.30        16.24        32.45        33.27        18.64        60.39 
TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OT 
       23.18         0.30         8.94        24.00         4.70         4.90 
TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH 
       29.00         2.60         7.40        55.50        35.97        12.92 
TCGA-L5-A8NJ TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-R6-A6DQ TCGA-R6-A6KZ 
       16.47        25.25        12.00        13.18         7.59         5.06 
TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW 
        6.35         2.89         1.45        20.38         4.80         9.27 
TCGA-V5-AASX TCGA-VR-A8ER TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 
        4.44        12.43        11.01         9.44         6.61        17.29 
TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8485 TCGA-BR-8678 
       19.33        35.24        18.71         2.66         9.21        11.54 
TCGA-BR-8683 TCGA-BR-A452 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        9.86         7.53        20.65        20.42         1.15        13.64 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        3.25         0.30         0.07         0.13         0.13         3.42 
TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-5719 TCGA-CG-5724 
       11.31        20.02         3.02        54.08         1.02        12.03 
TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        4.01        11.93        20.55        17.19        10.26        15.22 
TCGA-D7-8573 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-HU-8249 TCGA-HU-8604 
       19.50         7.40         0.62        16.24        14.17        12.10 
TCGA-HU-A4HD TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-VQ-A8DV 
       27.42        37.64         9.86        18.21         8.61        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A91A TCGA-VQ-A91Z 
       13.02         7.73        22.19         2.70        36.69        52.24 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6K 
        4.54        64.18        21.04        11.24        29.98        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`1P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94         4.21         7.69         6.21        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
        3.68        41.52        42.77        25.41        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J 
       25.22        24.03         6.28         3.16        30.25         4.31 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        3.32         7.17         1.38         3.16        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 
        7.43         6.94         8.71        25.12         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        3.02         2.66        13.48        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        5.49        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22         4.47        12.33        10.52        12.23        12.03 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 
        0.13        33.11         5.16         7.82         8.02        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
        7.04        29.59        53.95         9.30        15.78        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO 
        7.00        20.02         5.29         3.42        15.35        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        22.82         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91        10.16         3.42         2.10         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 
       19.73        26.70        11.70        19.56         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-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.76        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-8291 
        9.60        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-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-8486 TCGA-BR-8487 
       15.85         3.72         5.39        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-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        0.49        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-A4QL 
       12.82         0.66        19.36        13.51         0.46        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83        13.15        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-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         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 
           12.030            12.805 
[1] "0.1 - 64.2 (12.0)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         2        0        7        6        14         8
  1P LOSS WILD-TYPE       9       19       41       26        63        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           6         13         10          4       12
  1P LOSS WILD-TYPE        23         84         62         44       39
                   vv
clus                STAGE IVA
  1P LOSS MUTATED           1
  1P LOSS WILD-TYPE         3
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  2                 9
  STAGE IA                 0                19
  STAGE IB                 7                41
  STAGE II                 6                26
  STAGE IIA               14                63
  STAGE IIB                8                76
  STAGE III                6                23
  STAGE IIIA              13                84
  STAGE IIIB              10                62
  STAGE IIIC               4                44
  STAGE IV                12                39
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1P LOSS MUTATED       5  16  43  20
  1P LOSS WILD-TYPE    48 110 237 104
D42V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               5                48
  T2                 16               110
  T3                 43               237
  T4                 20               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
  1P LOSS MUTATED    28  26  17  11
  1P LOSS WILD-TYPE 172 156  79  86
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              28               172
  N1              26               156
  N2              17                79
  N3              11                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"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    67  11
  1P LOSS WILD-TYPE 446  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     67   11
  1P LOSS WILD-TYPE  446   28
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              67               446
  1              11                28
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    27  64
  1P LOSS WILD-TYPE 155 363
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     27   64
  1P LOSS WILD-TYPE  155  363
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              27               155
  MALE                64               363
[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                                                       19
  1P LOSS WILD-TYPE                                                    143
                   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                                                 17
  1P LOSS WILD-TYPE                                               61
                   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)                         19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               17
  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)                          143
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 61
  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  91
  1P LOSS WILD-TYPE   6 512
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   91
  1P LOSS WILD-TYPE    6  512
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                0                 6
  YES              91               512
[1] 2 2
[1] FALSE
D42V10, continuous
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    41   2   8   1
  1P LOSS WILD-TYPE 306  16  11  24
D42V11, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              41               306
  R1               2                16
  R2               8                11
  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"
D42V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED      17                         2
  1P LOSS WILD-TYPE   112                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           1    58
  1P LOSS WILD-TYPE                                         0   327
D42V13, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                                  17               112
  BLACK OR AFRICAN AMERICAN                               2                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  58               327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  53
  1P LOSS WILD-TYPE   7 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   53
  1P LOSS WILD-TYPE    7  341
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              53               341
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    24  21
  1Q LOSS WILD-TYPE 330 200
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               45               530 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21               200 
$`1Q LOSS MUTATED`
TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A88V 
       16.24        33.27         3.88         8.94        24.00         2.60 
TCGA-LN-A49O TCGA-LN-A5U7 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 
       13.41        25.25         7.59         5.06         6.35         2.89 
TCGA-R6-A8WC TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8ER TCGA-B7-A5TN TCGA-BR-4183 
        1.45         4.80         4.44        12.43         9.44         6.61 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-8289 TCGA-BR-A4PD TCGA-BR-A4PF 
       17.29        19.33        35.24         2.66        20.65         1.15 
TCGA-CD-5799 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-5724 TCGA-CG-5730 
        3.25         3.42        11.31        12.43        12.03         4.01 
TCGA-D7-6519 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-HU-8604 TCGA-HU-A4HD TCGA-IN-8663 
       20.55         7.40        16.24        12.10        27.42         3.39 
TCGA-IP-7968 TCGA-KB-A93H TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PE TCGA-VQ-A925 
        2.53        37.64        13.25        13.02        22.19         4.54 
TCGA-VQ-AA6B TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       29.98        12.43         0.79 

$`1Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       13.94         8.94         4.21        32.45         7.69         6.21 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF 
        6.28         3.16        30.25         0.30         4.31         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
       29.00         7.13         7.43         6.94         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        0.36         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.66        12.43         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02        14.70         7.04        29.59        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78        12.69         7.00        20.02        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        3.42        15.35         9.27        18.81        19.96        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       10.16         3.42         2.10         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       11.70        19.56        11.01         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-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-8291 
        9.60        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-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-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-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       19.36        13.51         0.46        20.42        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83        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-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        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-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-5725 
        1.02         0.99         6.02         0.99       105.07        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-D7-5577 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-D7-8576 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-5647 
        2.96        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-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-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-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-8462 
        9.67         8.88         8.81        21.21         3.45        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-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-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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        48.79         5.46        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-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       46.26        16.31         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        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-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-AA68 
        2.66        42.54        11.24        22.09        18.41        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       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 
            11.31             12.82 
[1] "0.8 - 37.6 (11.3)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.7"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        0        2        2         7         6
  1Q LOSS WILD-TYPE      11       19       46       30        70        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           2          5          7          2        4
  1Q LOSS WILD-TYPE        27         92         65         46       47
                   vv
clus                STAGE IVA
  1Q LOSS MUTATED           1
  1Q LOSS WILD-TYPE         3
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                11
  STAGE IA                 0                19
  STAGE IB                 2                46
  STAGE II                 2                30
  STAGE IIA                7                70
  STAGE IIB                6                78
  STAGE III                2                27
  STAGE IIIA               5                92
  STAGE IIIB               7                65
  STAGE IIIC               2                46
  STAGE IV                 4                47
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1Q LOSS MUTATED       1   6  23   9
  1Q LOSS WILD-TYPE    52 120 257 115
D43V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               1                52
  T2                  6               120
  T3                 23               257
  T4                  9               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
  1Q LOSS MUTATED    11  11  10   6
  1Q LOSS WILD-TYPE 189 171  86  91
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              11               189
  N1              11               171
  N2              10                86
  N3               6                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    28   5
  1Q LOSS WILD-TYPE 485  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     28    5
  1Q LOSS WILD-TYPE  485   34
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              28               485
  1               5                34
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    14  31
  1Q LOSS WILD-TYPE 168 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14   31
  1Q LOSS WILD-TYPE  168  396
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              14               168
  MALE                31               396
[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                                                       11
  1Q LOSS WILD-TYPE                                                    151
                   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)                         11
  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)                          151
  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  45
  1Q LOSS WILD-TYPE   6 558
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   45
  1Q LOSS WILD-TYPE    6  558
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                0                 6
  YES              45               558
[1] 2 2
[1] FALSE
D43V10, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    18   1   4   1
  1Q LOSS WILD-TYPE 329  17  15  24
D43V11, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              18               329
  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"
D43V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED       9                         1
  1Q LOSS WILD-TYPE   120                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0    30
  1Q LOSS WILD-TYPE                                         1   355
D43V13, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                                   9               120
  BLACK OR AFRICAN AMERICAN                               1                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  30               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  31
  1Q LOSS WILD-TYPE   7 363
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   31
  1Q LOSS WILD-TYPE    7  363
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              31               363
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    21  13
  2P LOSS WILD-TYPE 333 208
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               34               541 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               13               208 
$`2P LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-L5-A4OS TCGA-L5-A8NE TCGA-L5-A8NK TCGA-LN-A49L 
        2.63        20.12        58.59        55.50        13.55        10.45 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-R6-A8W8 TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-Z6-AAPN 
       10.52        12.23         2.89        18.81        42.87         2.66 
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-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 
        6.21        33.27        20.09         0.85        20.78        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
        0.10        13.25         0.10        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         4.44        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.10        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-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-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-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-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-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-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-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         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-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-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-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-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.36        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-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-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-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        5.52         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-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        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-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-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-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-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-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-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-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-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-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-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 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.13              0.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            58.59            122.30 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           12.545            12.790 
[1] "0.1 - 58.6 (12.5)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        0        4        2         6         6
  2P LOSS WILD-TYPE      11       19       44       30        71        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           0         12          2          3        2
  2P LOSS WILD-TYPE        29         85         70         45       49
                   vv
clus                STAGE IVA
  2P LOSS MUTATED           0
  2P LOSS WILD-TYPE         4
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                11
  STAGE IA                 0                19
  STAGE IB                 4                44
  STAGE II                 2                30
  STAGE IIA                6                71
  STAGE IIB                6                78
  STAGE III                0                29
  STAGE IIIA              12                85
  STAGE IIIB               2                70
  STAGE IIIC               3                45
  STAGE IV                 2                49
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2P LOSS MUTATED       0  13  18   6
  2P LOSS WILD-TYPE    53 113 262 118
D44V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               0                53
  T2                 13               113
  T3                 18               262
  T4                  6               118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P LOSS MUTATED    13  12   8   4
  2P LOSS WILD-TYPE 187 170  88  93
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              13               187
  N1              12               170
  N2               8                88
  N3               4                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"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    34   1
  2P LOSS WILD-TYPE 479  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     34    1
  2P LOSS WILD-TYPE  479   38
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              34               479
  1               1                38
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    14  24
  2P LOSS WILD-TYPE 168 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     14   24
  2P LOSS WILD-TYPE  168  403
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              14               168
  MALE                24               403
[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  36
  2P LOSS WILD-TYPE   4 567
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   36
  2P LOSS WILD-TYPE    4  567
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                2                 4
  YES              36               567
[1] 2 2
[1] FALSE
D44V10, continuous
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    21   3   1   0
  2P LOSS WILD-TYPE 326  15  18  25
D44V11, 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"
D44V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED       9                         1
  2P LOSS WILD-TYPE   120                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           0    24
  2P LOSS WILD-TYPE                                         1   361
D44V13, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                                   9               120
  BLACK OR AFRICAN AMERICAN                               1                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  24               361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  25
  2P LOSS WILD-TYPE   7 369
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   25
  2P LOSS WILD-TYPE    7  369
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              25               369
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    29  18
  2Q LOSS WILD-TYPE 325 203
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               47               528 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               203 
$`2Q LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A43H TCGA-L5-A4OS 
        2.63        20.12        18.64         0.79         0.30        58.59 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ 
        3.02        16.47        13.55        10.45        12.46        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-R6-A8W8 TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-Z6-AAPN 
       10.52        12.23         2.89        18.81        42.87         2.66 
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-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS 
        6.21        33.27        20.09         0.85        20.78         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16        30.25         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.95        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.48        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36         5.92        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35         0.10        13.25         0.10        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         4.44        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.10        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-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-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-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-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-A487 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       11.61         6.58        12.20         0.10        12.62         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-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-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        10.26        15.98        12.79        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-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-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-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
        0.23        18.08         1.51        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-A4GF TCGA-HU-A4GH 
       12.30        11.84        24.20         3.25        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-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-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-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-A6RP TCGA-IN-A6RR 
        3.39        18.38         5.36        13.08         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51         5.56         1.81        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-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        9.86        45.67         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-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        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-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-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-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-A94R TCGA-VQ-A94T 
        5.72        64.18        21.04         2.66        42.54        11.24 
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 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.13              0.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            58.59            122.30 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            12.46             12.79 
[1] "0.1 - 58.6 (12.5)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         1        2        4        2         8         7
  2Q LOSS WILD-TYPE      10       17       44       30        69        77
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           3         13          3          4        3
  2Q LOSS WILD-TYPE        26         84         69         44       48
                   vv
clus                STAGE IVA
  2Q LOSS MUTATED           0
  2Q LOSS WILD-TYPE         4
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                10
  STAGE IA                 2                17
  STAGE IB                 4                44
  STAGE II                 2                30
  STAGE IIA                8                69
  STAGE IIB                7                77
  STAGE III                3                26
  STAGE IIIA              13                84
  STAGE IIIB               3                69
  STAGE IIIC               4                44
  STAGE IV                 3                48
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2Q LOSS MUTATED       3  11  27   9
  2Q LOSS WILD-TYPE    50 115 253 115
D45V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               3                50
  T2                 11               115
  T3                 27               253
  T4                  9               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
  2Q LOSS MUTATED    19  15  10   6
  2Q LOSS WILD-TYPE 181 167  86  91
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              19               181
  N1              15               167
  N2              10                86
  N3               6                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    46   2
  2Q LOSS WILD-TYPE 467  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     46    2
  2Q LOSS WILD-TYPE  467   37
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              46               467
  1               2                37
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    14  37
  2Q LOSS WILD-TYPE 168 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     14   37
  2Q LOSS WILD-TYPE  168  390
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              14               168
  MALE                37               390
[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  49
  2Q LOSS WILD-TYPE   4 554
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   49
  2Q LOSS WILD-TYPE    4  554
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2                 4
  YES              49               554
[1] 2 2
[1] FALSE
D45V10, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    25   3   2   0
  2Q LOSS WILD-TYPE 322  15  17  25
D45V11, 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"
D45V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED      15                         2
  2Q LOSS WILD-TYPE   114                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           0    28
  2Q LOSS WILD-TYPE                                         1   357
D45V13, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                                  15               114
  BLACK OR AFRICAN AMERICAN                               2                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  28               357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  32
  2Q LOSS WILD-TYPE   7 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   32
  2Q LOSS WILD-TYPE    7  362
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              32               362
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   113  60
  3P LOSS WILD-TYPE 241 161
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              173               402 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               60               161 
$`3P LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3Y9 
       14.30         5.92        13.94         4.21        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
       20.78         2.63        20.12         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD 
        0.79        23.41         9.96        14.50        12.16        68.02 
TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
       25.41        30.25         8.94         4.70        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.32         7.17         7.13         7.43         6.94         2.60 
TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         2.66        35.97        12.92        16.47        13.55 
TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       13.41         5.92        12.43        13.41        13.15        15.35 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-RE-A7BO 
        0.13        33.11         7.59         7.04         6.35         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EU 
       20.02        20.38         3.42        18.81        19.96        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91        10.16         3.42         2.10         2.66 
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-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8526 
       13.51        20.65        20.42         1.15        13.64         0.07 
TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A48A TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 
        0.07         0.13        12.43        20.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5730 
       54.08         4.01        12.03        18.97        15.02         4.01 
TCGA-D7-5578 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-A6EX TCGA-EQ-5647 
       12.66        13.35        17.19        15.22        11.31         0.62 
TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF 
        7.99        19.53        14.07        17.06         0.56         5.52 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-IN-7806 
       12.59        14.17         3.25         6.25        23.84        21.21 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A93H 
        1.41         6.44        12.59         6.51         5.56        37.64 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-RD-A8N6 
        9.86        45.67        18.21         8.52        16.67         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
        5.79        13.25        18.48        34.45        22.19         2.70 
TCGA-VQ-A8PY TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-A94R TCGA-VQ-A94U 
       14.33        36.16         9.50         4.54        42.54        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       18.41        32.94        29.98        12.43         0.79 

$`3P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55         7.63         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-IG-A4QT 
       32.45         7.69         6.21        33.27        18.64         9.30 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       12.82        14.86         4.67       122.10        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        42.77        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
       25.22        24.03         6.28         3.16         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
       24.00         3.68        19.99        47.93        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W 
        3.16        58.59         4.90        29.00         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL 
        0.36         3.95         3.02        55.50        13.48        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       52.57        46.09        10.36        10.45        12.66         0.10 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A9 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10        13.25        12.59        11.54         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         5.06        14.70        29.59        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RE 
       15.78         2.89         1.45        12.69         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
       15.35         9.27         4.44        22.82        12.43         1.55 
TCGA-VR-A8EX TCGA-VR-AA7B TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       28.11        11.24        19.73        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.87        13.68        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-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-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       23.93        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       12.76        14.43        11.44        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        12.95        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-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-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        12.56        13.87         6.08        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
        8.98        14.17        12.82         0.66        19.36         0.46 
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-8528 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 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-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 
       12.62         3.02        27.02        15.95         1.02        14.01 
TCGA-CG-4443 TCGA-CG-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-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-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.36        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        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-D7-8576 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-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-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.40         7.13        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       11.38         3.48        22.29        59.54         5.03        13.58 
TCGA-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-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-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84        24.20        22.75        25.81        11.77 
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-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        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-A6RR TCGA-IN-A7NT 
       18.38         5.36         5.19        13.08         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-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-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-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 
       19.04         0.92        48.79         5.46        13.02        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-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       46.26        16.31         2.50        12.79        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-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-A91E TCGA-VQ-A91K 
       64.57        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       18.74        20.81        22.68         1.71         7.36         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-AA68 TCGA-VQ-AA69 
       64.18        21.04         2.66        11.24        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 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            68.02            122.30 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           12.590            12.805 
[1] "0.1 - 68.0 (12.6)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         4        4       12        6        32        27
  3P LOSS WILD-TYPE       7       15       36       26        45        57
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED          11         31         16         11       15
  3P LOSS WILD-TYPE        18         66         56         37       36
                   vv
clus                STAGE IVA
  3P LOSS MUTATED           1
  3P LOSS WILD-TYPE         3
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  4                 7
  STAGE IA                 4                15
  STAGE IB                12                36
  STAGE II                 6                26
  STAGE IIA               32                45
  STAGE IIB               27                57
  STAGE III               11                18
  STAGE IIIA              31                66
  STAGE IIIB              16                56
  STAGE IIIC              11                37
  STAGE IV                15                36
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3P LOSS MUTATED      18  34  89  31
  3P LOSS WILD-TYPE    35  92 191  93
D46V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              18                35
  T2                 34                92
  T3                 89               191
  T4                 31                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
  3P LOSS MUTATED    66  53  34  17
  3P LOSS WILD-TYPE 134 129  62  80
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              66               134
  N1              53               129
  N2              34                62
  N3              17                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"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   146  14
  3P LOSS WILD-TYPE 367  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    146   14
  3P LOSS WILD-TYPE  367   25
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             146               367
  1              14                25
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    47 130
  3P LOSS WILD-TYPE 135 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     47  130
  3P LOSS WILD-TYPE  135  297
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              47               135
  MALE               130               297
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3P LOSS MUTATED                                       7
  3P LOSS WILD-TYPE                                    64
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                       33
  3P LOSS WILD-TYPE                                                    129
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                                  25
  3P LOSS WILD-TYPE                                                                56
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  3P LOSS MUTATED                                                 18
  3P LOSS WILD-TYPE                                               60
                   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                                           7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               18
  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                                            64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 60
  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     1 176
  3P LOSS WILD-TYPE   5 427
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1  176
  3P LOSS WILD-TYPE    5  427
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                1                 5
  YES             176               427
[1] 2 2
[1] FALSE
D46V10, continuous
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    75   3   5   1
  3P LOSS WILD-TYPE 272  15  14  24
D46V11, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              75               272
  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"
D46V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED      47                         3
  3P LOSS WILD-TYPE    82                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           0   106
  3P LOSS WILD-TYPE                                         1   279
D46V13, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                                  47                82
  BLACK OR AFRICAN AMERICAN                               3                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 106               279
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1 113
  3P LOSS WILD-TYPE   6 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1  113
  3P LOSS WILD-TYPE    6  281
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO             113               281
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    53  32
  3Q LOSS WILD-TYPE 301 189
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               85               490 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               32               189 
$`3Q LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YA 
       14.30         5.92        13.94         4.21        32.45        20.78 
TCGA-IG-A5S3 TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OX TCGA-L5-A8NH 
       23.41        25.41        30.25        32.61         7.43        12.92 
TCGA-LN-A49K TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U5 TCGA-LN-A5U6 
        5.92        15.35        12.46         0.10         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A9FO TCGA-R6-A6XQ TCGA-RE-A7BO TCGA-VR-A8EP 
       25.25        12.23         0.13         6.35         7.00        19.96 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-A5TJ 
       18.18        46.19        10.16         3.42         2.10        11.01 
TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8058 
       17.29        35.24        15.42        28.01        18.71        17.49 
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-8526 TCGA-CD-A48A TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 
       13.64         0.07        12.43        54.08         4.01        18.97 
TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-A6EX TCGA-EQ-5647 TCGA-FP-7829 
       15.02        12.66        17.19        11.31         0.62        19.53 
TCGA-FP-8099 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GU TCGA-IN-7806 
       17.06         5.52        14.17         3.25         6.25        21.21 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 
        1.41        12.59         6.51         5.56        37.64         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8PE 
       45.67        18.21         8.52        13.25        34.45        22.19 
TCGA-VQ-A8PY TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA6B 
       14.33        36.16         9.50        42.54        22.09        29.98 
TCGA-VQ-AA6K 
       12.43 

$`3Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55         7.63         8.94        16.24 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB 
        7.69         6.21        33.27        20.09         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       12.16       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        42.77        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       24.03         6.28         3.16         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
       24.00         3.68         4.70        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        46.09        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41         0.10        13.15         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW 
       15.52        11.54        12.33        13.22        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        13.18        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        7.59         5.06        14.70         7.04        29.59        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
        9.30        15.78         2.89         1.45        12.69        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        30.71        42.87        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        9.17        15.91         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-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-7957 TCGA-BR-7958 TCGA-BR-8059 
       28.73        12.43         3.45         9.07        12.76        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-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95        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-8484 TCGA-BR-8487 
       14.79         0.26        15.85         3.72        25.18         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-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        12.56        13.87         6.08         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-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-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-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        7.99         8.05        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-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-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        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-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       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-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-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        4.34         7.40         7.13         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-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-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-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20        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-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-A6RP TCGA-IN-A6RR 
       18.38         5.36         5.19        13.08         6.44         6.74 
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-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       20.15         3.72        19.73        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-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-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-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-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-A91E TCGA-VQ-A91K 
       64.57        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       18.74        20.81        22.68         1.71         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 
             0.07              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            54.08            122.30 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           12.920            12.725 
[1] "0.1 - 54.1 (12.9)"  "0.0 - 122.3 (12.7)"
[1] "hr=" "1"  
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        3        4        2        13        17
  3Q LOSS WILD-TYPE       9       16       44       30        64        67
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           3         17          9          5       11
  3Q LOSS WILD-TYPE        26         80         63         43       40
                   vv
clus                STAGE IVA
  3Q LOSS MUTATED           0
  3Q LOSS WILD-TYPE         4
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                 9
  STAGE IA                 3                16
  STAGE IB                 4                44
  STAGE II                 2                30
  STAGE IIA               13                64
  STAGE IIB               17                67
  STAGE III                3                26
  STAGE IIIA              17                80
  STAGE IIIB               9                63
  STAGE IIIC               5                43
  STAGE IV                11                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3Q LOSS MUTATED      10  10  46  21
  3Q LOSS WILD-TYPE    43 116 234 103
D47V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1              10                43
  T2                 10               116
  T3                 46               234
  T4                 21               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
  3Q LOSS MUTATED    30  27  19  10
  3Q LOSS WILD-TYPE 170 155  77  87
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              30               170
  N1              27               155
  N2              19                77
  N3              10                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"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    77   9
  3Q LOSS WILD-TYPE 436  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     77    9
  3Q LOSS WILD-TYPE  436   30
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              77               436
  1               9                30
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    24  65
  3Q LOSS WILD-TYPE 158 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     24   65
  3Q LOSS WILD-TYPE  158  362
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              24               158
  MALE                65               362
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3Q LOSS MUTATED                                       3
  3Q LOSS WILD-TYPE                                    68
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                       24
  3Q LOSS WILD-TYPE                                                    138
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                                  14
  3Q LOSS WILD-TYPE                                                                67
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  3Q LOSS MUTATED                                                 12
  3Q LOSS WILD-TYPE                                               66
                   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                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              14
  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                                                                  3Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                67
  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"
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  89
  3Q LOSS WILD-TYPE   6 514
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   89
  3Q LOSS WILD-TYPE    6  514
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                 6
  YES              89               514
[1] 2 2
[1] FALSE
D47V10, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    47   3   2   1
  3Q LOSS WILD-TYPE 300  15  17  24
D47V11, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              47               300
  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"
D47V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED      21                         1
  3Q LOSS WILD-TYPE   108                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           0    56
  3Q LOSS WILD-TYPE                                         1   329
D47V13, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                                  21               108
  BLACK OR AFRICAN AMERICAN                               1                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  56               329
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  59
  3Q LOSS WILD-TYPE   6 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   59
  3Q LOSS WILD-TYPE    6  335
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              59               335
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   145 104
  4P LOSS WILD-TYPE 209 117
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              249               326 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              104               117 
$`4P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       20.78        20.12        18.64         3.88         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB 
       12.82         9.96         4.67        12.16        44.75        60.39 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE 
       42.77        23.18        25.22         3.16         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        4.70        21.01         3.16         4.90         7.13         7.43 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         3.95        35.97        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.22         8.71        13.41        27.12        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U 
        5.92        10.45        12.66        12.43         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.25         0.10        12.59        12.49        12.76         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.00        12.23        13.18         0.13         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        5.06         7.04         6.35         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP 
        7.00        20.38         3.42         4.80         9.27        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I 
       18.18        42.87        46.19        15.06        11.24        15.91 
TCGA-Z6-A8JD TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4279 TCGA-BR-6456 
        3.42        11.01         9.44         6.61         9.57        17.29 
TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 
        9.17        31.20         9.21        35.24        18.15        28.73 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 
        9.07        18.71        17.49         0.69         9.60         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 
       16.31         2.20        15.58         7.40        19.50        22.19 
TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
       17.52        14.04        14.79         3.72         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 
       20.22         0.49        11.54         9.86        10.68         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD 
       22.26         1.48         0.72         0.66        13.51        20.65 
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-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.13         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       11.61        12.20        20.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 
        4.01        47.05        19.07        12.03        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 
       30.97        15.02        79.07        19.13        20.55        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YU 
       10.26        15.22        11.31        19.50        18.21        16.44 
TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 
       11.31         7.40         0.62         7.99        11.38        14.07 
TCGA-FP-8099 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       17.06         5.52         0.23        26.47         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP 
       12.59        14.17        12.10        22.75        25.81         8.98 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.25         0.26         2.10        12.95        23.84         9.67 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
       27.42        18.81         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-A8PK TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N 
       12.79         2.70        17.85        65.16        36.69        18.74 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       36.16         9.50         9.73        52.24         9.04         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6B 
       21.04        42.54        11.24        22.09        32.94        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       54.12        16.14        21.11 

$`4P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YB TCGA-IG-A4QT 
       31.27         7.63         7.69         6.21         2.63         9.30 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD 
       17.03        23.41        14.86        14.50       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
        3.68        41.52        25.41        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28        30.25         0.30         4.31         3.68        32.61 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       58.59        29.00         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM 
        0.36         3.02        55.50         2.66        13.48         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49O TCGA-LN-A49S 
        5.49        21.37        83.24        52.57        13.41        13.15 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A5U5 
        0.10        12.46        12.59        22.39        11.54         4.47 
TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG 
       12.03        33.11         5.16         7.82        14.70        29.59 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV 
       53.95         9.30        15.78        20.02         5.29        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EY TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE 
        4.44        18.81        30.71         9.17        10.16         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        19.56         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
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-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-6852 TCGA-BR-7196 
       12.16         8.98        21.11        30.90        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 
       24.76        23.93        15.42        28.01        15.32        12.43 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 
        3.45        12.76        14.43        11.44        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
        8.05         0.56        12.95         6.18        13.08         0.26 
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-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.26        15.85        25.18         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 
        9.34        13.45         6.28         7.53        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
       15.68         8.22        12.56        13.87         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-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36         0.46        20.42         1.15        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 
        2.83        13.15        13.18         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG 
        0.13         0.16         0.10         0.10         3.42         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-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 
       14.01        29.98        21.99         0.00         9.01        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-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        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-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       18.84        18.54        18.61        17.85        13.35        15.98 
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-HU-8244 
       59.54         5.03        13.58         0.56        18.08        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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20         3.25        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.10         6.51        10.19        19.36        12.30         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
        8.81        21.21         3.45         3.39        18.38         5.19 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
       13.08        12.59         6.51         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF 
       13.51        20.15        37.64         3.72        19.73         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
       61.25         4.60         8.61         5.13       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
      116.38        71.38        57.44        16.87        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       48.79        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D 
       13.35        26.24        27.35        64.57        14.33        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       11.93        61.22        20.81        22.68         1.71         7.36 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        64.18         2.66 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K 
       18.41        40.08        28.41        17.13        26.04        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       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 
           12.430            13.115 
[1] "0.1 - 115.7 (12.4)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1.3"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         4        3       17       17        39        32
  4P LOSS WILD-TYPE       7       16       31       15        38        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED          17         44         32         20       18
  4P LOSS WILD-TYPE        12         53         40         28       33
                   vv
clus                STAGE IVA
  4P LOSS MUTATED           2
  4P LOSS WILD-TYPE         2
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  4                 7
  STAGE IA                 3                16
  STAGE IB                17                31
  STAGE II                17                15
  STAGE IIA               39                38
  STAGE IIB               32                52
  STAGE III               17                12
  STAGE IIIA              44                53
  STAGE IIIB              32                40
  STAGE IIIC              20                28
  STAGE IV                18                33
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4P LOSS MUTATED      18  52 133  46
  4P LOSS WILD-TYPE    35  74 147  78
D48V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              18                35
  T2                 52                74
  T3                133               147
  T4                 46                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
  4P LOSS MUTATED    80  79  48  38
  4P LOSS WILD-TYPE 120 103  48  59
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              80               120
  N1              79               103
  N2              48                48
  N3              38                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"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   226  13
  4P LOSS WILD-TYPE 287  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    226   13
  4P LOSS WILD-TYPE  287   26
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             226               287
  1              13                26
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    70 193
  4P LOSS WILD-TYPE 112 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     70  193
  4P LOSS WILD-TYPE  112  234
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              70               112
  MALE               193               234
[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                                                       55
  4P LOSS WILD-TYPE                                                    107
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                                  38
  4P LOSS WILD-TYPE                                                                43
                   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)                         55
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  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)                          107
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                43
  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     3 260
  4P LOSS WILD-TYPE   3 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3  260
  4P LOSS WILD-TYPE    3  343
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                3                 3
  YES             260               343
[1] 2 2
[1] FALSE
D48V10, continuous
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED   129   7   6   8
  4P LOSS WILD-TYPE 218  11  13  17
D48V11, 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"
D48V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED      66                         6
  4P LOSS WILD-TYPE    63                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           0   153
  4P LOSS WILD-TYPE                                         1   232
D48V13, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                                  66                63
  BLACK OR AFRICAN AMERICAN                               6                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 153               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"
D48V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     2 164
  4P LOSS WILD-TYPE   5 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2  164
  4P LOSS WILD-TYPE    5  230
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             164               230
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   132 103
  4Q LOSS WILD-TYPE 222 118
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              235               340 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              103               118 
$`4Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6FA 
        3.88         0.53         0.79        12.82         4.67        44.75 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43J 
       60.39        42.77        23.18        25.22         3.16         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
        8.94        24.00         4.70         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH 
        7.43         6.94         7.40         3.95        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       16.47        13.22         8.71        13.41        27.12        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       46.09        10.36         5.92        10.45        12.66         0.10 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       15.35        13.25        12.59        12.76         0.10        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
       13.18         8.02         7.59         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30         2.89         1.45        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
       20.38         4.80         9.27        19.96        22.82         1.55 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-B7-A5TJ 
       28.11        18.18        42.87        11.24        15.91        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6803 
        9.44         6.61        17.29        19.33         9.17        31.20 
TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       35.24        18.15        28.73         9.07        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       14.43         0.69         9.60         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 
       15.58         7.40        19.50        22.19        17.52        14.04 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 
       14.79         3.72         5.39         9.21        20.22         0.49 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       11.54         9.86        10.68         7.53        22.26         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.72         0.66        13.51        20.65         1.15        13.64 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        3.25         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.13         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       11.61        12.20        20.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 
        4.01        47.05        19.07        12.03        18.97        30.97 
TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6518 TCGA-D7-6519 
       15.02        79.07         4.01        69.04        19.13        20.55 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8573 
       17.19        10.26        15.22        15.98        11.31        19.50 
TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       18.21        16.44        11.31         7.40         0.62         7.99 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 
       11.38        14.07        17.06         5.52         0.23         1.51 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU 
        5.92        12.59        12.10        22.75         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-IN-A7NT TCGA-IP-7968 TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        5.56         2.53         9.86        45.67        18.21         6.08 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
        9.24        11.05        16.67        37.91       115.69         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       35.61         5.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       35.24        21.73         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N 
        2.70        17.85        13.35        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-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YB 
       31.27         7.63         7.69         6.21        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12        18.64         9.30        17.03        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86        14.50        12.16       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        25.41        21.70        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       30.25         0.30         3.68        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 
       29.00         8.71         2.60        25.12         0.36         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       55.50         2.66        13.48        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V 
       21.37        52.57        12.43        13.41        13.15         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10        12.46        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       11.54        13.22        12.03         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB 
        7.82        14.70        53.95        15.78        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU 
        3.42        15.35         4.44        18.81        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
        8.12        30.71        46.19        15.06         9.17        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-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-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-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-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-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8060 
       28.01        15.32        12.43         3.45        12.76        11.44 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8360 
       12.26        20.55         8.05         0.56        12.95         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       13.08         0.26         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8487 
       11.80        19.17         0.26        15.85        25.18         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-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-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL 
        0.53        12.82        19.36         0.46        20.42        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8528 
        5.13         2.83        13.15        13.18         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG 
        0.13         0.16         0.10         0.10         3.42         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-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       14.01        29.98        21.99         0.00         9.01         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-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       21.07         7.99        12.36        12.66        11.93        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-6818 
       18.54        18.61        17.85        13.35        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-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 
       13.58         0.56        18.08        26.47        14.27        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-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 
       29.98         0.10         6.51        10.19        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL 
        8.88         8.81        21.21         3.45        18.38         5.19 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       13.08        12.59         6.51         1.81         7.82        13.51 
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-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        8.52        61.25         4.60         8.61         5.13       122.30 
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-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
        0.92        48.79        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       34.29        16.31         2.50         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D 
       15.65        26.24        27.35        64.57        14.33        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-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        7.36         2.01        55.43         6.58         5.72        64.18 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        11.24        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        10.62         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 
           12.200            13.165 
[1] "0.1 - 115.7 (12.2)" "0.0 - 122.3 (13.2)"
[1] "hr=" "1.4"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         3        3       15       16        31        32
  4Q LOSS WILD-TYPE       8       16       33       16        46        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED          17         40         31         20       19
  4Q LOSS WILD-TYPE        12         57         41         28       32
                   vv
clus                STAGE IVA
  4Q LOSS MUTATED           2
  4Q LOSS WILD-TYPE         2
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  3                 8
  STAGE IA                 3                16
  STAGE IB                15                33
  STAGE II                16                16
  STAGE IIA               31                46
  STAGE IIB               32                52
  STAGE III               17                12
  STAGE IIIA              40                57
  STAGE IIIB              31                41
  STAGE IIIC              20                28
  STAGE IV                19                32
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4Q LOSS MUTATED      14  48 124  46
  4Q LOSS WILD-TYPE    39  78 156  78
D49V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              14                39
  T2                 48                78
  T3                124               156
  T4                 46                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
  4Q LOSS MUTATED    69  77  45  38
  4Q LOSS WILD-TYPE 131 105  51  59
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              69               131
  N1              77               105
  N2              45                51
  N3              38                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"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   208  14
  4Q LOSS WILD-TYPE 305  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    208   14
  4Q LOSS WILD-TYPE  305   25
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             208               305
  1              14                25
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    70 177
  4Q LOSS WILD-TYPE 112 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     70  177
  4Q LOSS WILD-TYPE  112  250
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              70               112
  MALE               177               250
[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                                                                  39
  4Q LOSS WILD-TYPE                                                                42
                   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)              39
  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)                42
  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     3 244
  4Q LOSS WILD-TYPE   3 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3  244
  4Q LOSS WILD-TYPE    3  359
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                3                 3
  YES             244               359
[1] 2 2
[1] FALSE
D49V10, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED   128   7   7   6
  4Q LOSS WILD-TYPE 219  11  12  19
D49V11, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             128               219
  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"
D49V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED      59                         5
  4Q LOSS WILD-TYPE    70                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           0   149
  4Q LOSS WILD-TYPE                                         1   236
D49V13, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                                  59                70
  BLACK OR AFRICAN AMERICAN                               5                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 149               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"
D49V14, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     3 153
  4Q LOSS WILD-TYPE   4 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3  153
  4Q LOSS WILD-TYPE    4  241
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             153               241
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    60  47
  5P LOSS WILD-TYPE 294 174
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              107               468 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               47               174 
$`5P LOSS MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3QL 
       58.55         7.63        13.94         8.94         4.21        20.09 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB 
        3.88         0.53        17.03         4.67       122.10        60.39 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OS 
       30.25        24.00         3.68         4.70        21.01        58.59 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NR 
        2.60         3.95         3.02         2.66         5.49         8.71 
TCGA-L5-A8NT TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A4A8 TCGA-LN-A7HV 
       27.12         5.92        10.45         0.10        15.52        10.52 
TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
       33.11        29.59         6.35         9.30         2.89         1.45 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER 
       12.69        20.02         9.27         4.44        22.82        12.43 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6458 
       46.19        10.16        11.01         9.44         6.61        19.33 
TCGA-BR-6565 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8483 
        9.17        12.76        18.71         2.20        14.04         5.39 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        9.86        10.68         7.53        22.26         1.48         0.72 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-8535 TCGA-CD-A4MH TCGA-CG-4440 
       20.42        13.64        13.15         0.13        12.20         4.01 
TCGA-CG-4449 TCGA-D7-6520 TCGA-D7-6815 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 
       19.07        18.84        15.98         7.99        72.23         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
        5.52         5.92         0.76        11.77         8.98         6.25 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL 
       12.95        23.84         9.67        21.21        18.81         5.19 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZF 
       13.08         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-A91V TCGA-VQ-A91Y 
       12.79         2.70        13.35         1.71        36.16         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-ZQ-A9CR 
       52.24         9.04        21.04        42.54         0.79 

$`5P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        31.27        14.30         5.92        16.24        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
       20.12        18.64         9.30         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        4.31         8.94        32.61        19.99        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         7.43         6.94         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40        55.50        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55        13.22         7.76        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09        10.36        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.10        13.15        15.35        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU 
       12.00        12.23        12.03        13.18         0.13         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       53.95        15.78         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU 
        4.80        15.35        18.81        19.96         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        30.71        18.18        42.87        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       11.24         9.17        15.91         3.42         2.10         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 
       19.73        26.70        11.70        19.56         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-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        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-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        9.07        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-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-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-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72        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-A44T 
       11.54        15.81        16.44        15.68         8.22        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       13.87         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-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65         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-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-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-8245 TCGA-HU-8249 
       18.08        26.47         1.51        14.27        12.59        14.17 
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-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-A4H0 
       29.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       19.36        12.30         8.88         8.81        27.42         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39        18.38         5.36         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-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        20.15         3.72        19.73        45.67        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-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       57.44         8.94        35.61        16.87        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.25        18.48        35.24        21.73 
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-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.50        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        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-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       22.68         7.36         9.50         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
        6.58         5.72        64.18         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 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              0.1               0.0 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            122.1             122.3 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           10.160            13.115 
[1] "0.1 - 122.1 (10.2)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1.3"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         7        3        3        2        11        19
  5P LOSS WILD-TYPE       4       16       45       30        66        65
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           9         19         11          7        6
  5P LOSS WILD-TYPE        20         78         61         41       45
                   vv
clus                STAGE IVA
  5P LOSS MUTATED           1
  5P LOSS WILD-TYPE         3
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  7                 4
  STAGE IA                 3                16
  STAGE IB                 3                45
  STAGE II                 2                30
  STAGE IIA               11                66
  STAGE IIB               19                65
  STAGE III                9                20
  STAGE IIIA              19                78
  STAGE IIIB              11                61
  STAGE IIIC               7                41
  STAGE IV                 6                45
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5P LOSS MUTATED      18  14  47  21
  5P LOSS WILD-TYPE    35 112 233 103
D50V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              18                35
  T2                 14               112
  T3                 47               233
  T4                 21               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
  5P LOSS MUTATED    28  40  16  14
  5P LOSS WILD-TYPE 172 142  80  83
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              28               172
  N1              40               142
  N2              16                80
  N3              14                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"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    89   5
  5P LOSS WILD-TYPE 424  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     89    5
  5P LOSS WILD-TYPE  424   34
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              89               424
  1               5                34
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    29  81
  5P LOSS WILD-TYPE 153 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     29   81
  5P LOSS WILD-TYPE  153  346
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              29               153
  MALE                81               346
[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                                                       23
  5P LOSS WILD-TYPE                                                    139
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                                  12
  5P LOSS WILD-TYPE                                                                69
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5P LOSS MUTATED                                                 21
  5P LOSS WILD-TYPE                                               57
                   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)                         23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               21
  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)                          139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 57
  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     0 110
  5P LOSS WILD-TYPE   6 493
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0  110
  5P LOSS WILD-TYPE    6  493
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                0                 6
  YES             110               493
[1] 2 2
[1] FALSE
D50V10, continuous
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    50   2   4   3
  5P LOSS WILD-TYPE 297  16  15  22
D50V11, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              50               297
  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"
D50V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED      24                         5
  5P LOSS WILD-TYPE   105                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           0    67
  5P LOSS WILD-TYPE                                         1   318
D50V13, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                                  24               105
  BLACK OR AFRICAN AMERICAN                               5                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  67               318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     2  67
  5P LOSS WILD-TYPE   5 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   67
  5P LOSS WILD-TYPE    5  327
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              67               327
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   105  78
  5Q LOSS WILD-TYPE 249 143
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              183               392 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               78               143 
$`5Q LOSS MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       32.45        20.09         2.63        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH 
        0.53         4.67        14.50       122.10        60.39        42.77 
TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ 
       31.56        30.25        24.00         3.68         4.70        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
       47.93         7.17         3.16        58.59         4.90         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         0.36         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       35.97        12.92        13.55         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49U 
       27.12        52.57         5.92        10.45        12.43        15.35 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HV 
       12.49        22.39        15.52        12.33        12.33        10.52 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
       13.18        33.11         5.16        29.59         6.35         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASW 
        2.89         1.45        12.69        20.02        20.38         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW 
        4.44        18.81        19.96        22.82        12.43         8.12 
TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-B7-A5TJ 
       28.11        42.87        46.19        10.16         2.66        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 
        9.44         6.61        19.33         9.17         9.21        35.24 
TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8289 
       28.01         3.45        12.76        18.71        12.95         2.66 
TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8678 TCGA-BR-8683 
        2.20        14.04        14.79         5.39        11.54         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        8.22        10.68         7.53        22.26         1.48         0.72 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8526 
       20.42        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-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-5718 
       27.02        54.08         4.01        47.05        19.07        36.00 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 
       11.93        18.84        10.26        15.98        12.79        12.33 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF 
       11.31         2.96         7.99        72.23         0.56         5.52 
TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP 
        5.92         0.76         3.25        22.75        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
        6.25        12.95        23.84         9.67        27.42        21.21 
TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-AB1V TCGA-KB-A6F7 
       18.81         5.19        13.08         6.44         7.82        60.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A8MW 
       37.64         9.86        18.21         8.52         6.08        37.91 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        8.94         5.79         5.46        13.25        13.02        35.24 
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-A8PS TCGA-VQ-A8PU TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A91Z 
       13.35        27.35         1.71        36.16         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 
        9.04         2.01         4.54        21.04        42.54        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-ZQ-A9CR 
       32.94        17.13         0.79 

$`5Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IC-A6RE TCGA-IC-A6RF 
       25.78        31.27        14.30         5.92         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       33.27         0.85        20.78         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA 
       23.41        12.82         9.96        14.86        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        25.41        21.70        23.18 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
       25.22        24.03         6.28         3.16         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        8.94        32.61        19.99        18.35         3.32         1.38 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43         6.94         8.71        25.12         7.40 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.48        16.47        13.22         7.76        21.37        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       46.09        10.36        12.66        13.41         0.10        13.15 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
        0.10        13.25         0.10        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59         0.10        11.54        13.22         4.47        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.00        12.23        12.03         0.13         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 
        7.59         5.06        14.70         7.04        53.95        15.78 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET 
        7.00         5.29         3.42         4.80        15.35         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.31        30.71        18.18        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
       15.91         3.42         2.10        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.87        17.29        13.68        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-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       15.42        18.15        15.32        28.73        12.43         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-8291 TCGA-BR-8296 TCGA-BR-8297 
       20.55         8.05         0.56        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-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-A44T 
        7.53         0.49        15.81        16.44        15.68        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       13.87         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-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65         1.15        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8529 
        3.25         0.30         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.10         3.42         9.34 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43         6.58         0.10        12.62        20.02         3.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         7.99         8.05        14.01        29.98 
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-5719 TCGA-CG-5720 
       12.00        22.98        30.97         6.97         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-D7-6521 TCGA-D7-6522 
       12.36        12.66        19.13        20.55        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 
       17.85        13.35        17.19        15.22        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-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-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-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-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       12.30        11.84        24.20        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        0.10         6.51        10.19         0.26         2.10        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       12.30         8.88         8.81         3.45         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        5.36         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 
            122.1             122.3 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           12.330            12.985 
[1] "0.1 - 122.1 (12.3)" "0.0 - 122.3 (13.0)"
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         7        7        9        8        20        29
  5Q LOSS WILD-TYPE       4       12       39       24        57        55
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED          11         40         18         12       10
  5Q LOSS WILD-TYPE        18         57         54         36       41
                   vv
clus                STAGE IVA
  5Q LOSS MUTATED           3
  5Q LOSS WILD-TYPE         1
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  7                 4
  STAGE IA                 7                12
  STAGE IB                 9                39
  STAGE II                 8                24
  STAGE IIA               20                57
  STAGE IIB               29                55
  STAGE III               11                18
  STAGE IIIA              40                57
  STAGE IIIB              18                54
  STAGE IIIC              12                36
  STAGE IV                10                41
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5Q LOSS MUTATED      24  34  87  32
  5Q LOSS WILD-TYPE    29  92 193  92
D51V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              24                29
  T2                 34                92
  T3                 87               193
  T4                 32                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
  5Q LOSS MUTATED    55  67  31  21
  5Q LOSS WILD-TYPE 145 115  65  76
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              55               145
  N1              67               115
  N2              31                65
  N3              21                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"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   156  10
  5Q LOSS WILD-TYPE 357  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    156   10
  5Q LOSS WILD-TYPE  357   29
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0             156               357
  1              10                29
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    51 136
  5Q LOSS WILD-TYPE 131 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     51  136
  5Q LOSS WILD-TYPE  131  291
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              51               131
  MALE               136               291
[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                                                       37
  5Q LOSS WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                                  23
  5Q LOSS WILD-TYPE                                                                58
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5Q LOSS MUTATED                                                 33
  5Q LOSS WILD-TYPE                                               45
                   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                                                           2
  5Q LOSS WILD-TYPE                                                         6
                   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)                         37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  5Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  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"
D51V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1 186
  5Q LOSS WILD-TYPE   5 417
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1  186
  5Q LOSS WILD-TYPE    5  417
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                1                 5
  YES             186               417
[1] 2 2
[1] FALSE
D51V10, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    88   4   5   3
  5Q LOSS WILD-TYPE 259  14  14  22
D51V11, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              88               259
  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"
D51V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED      43                         5
  5Q LOSS WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           0   116
  5Q LOSS WILD-TYPE                                         1   269
D51V13, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                                  43                86
  BLACK OR AFRICAN AMERICAN                               5                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 116               269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     2 108
  5Q LOSS WILD-TYPE   5 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2  108
  5Q LOSS WILD-TYPE    5  286
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             108               286
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    55  32
  6P LOSS WILD-TYPE 299 189
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               87               488 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               32               189 
$`6P LOSS MUTATED`
TCGA-2H-A9GK TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A5S3 TCGA-JY-A6FB 
        7.63        33.27        20.09         0.53        23.41        60.39 
TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OR 
       23.18         3.16         4.31         8.94         4.70         3.16 
TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K 
        0.36        16.47        13.55        83.24        52.57         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A5U7 
       12.43        13.41        13.25        12.59        12.49        25.25 
TCGA-LN-A7HZ TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RC TCGA-V5-AASW 
       13.18         1.45        12.69        20.02         3.42         9.27 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-Z6-A8JD TCGA-Z6-AAPN 
       22.82        12.43         8.12        18.18         3.42         2.66 
TCGA-ZR-A9CJ TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7716 TCGA-BR-A4CQ TCGA-BR-A4J1 
       19.73         6.18        17.29        28.01        22.26         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 
       13.51        20.65         1.15         0.16         0.10         0.13 
TCGA-CD-A48A TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6519 
       12.43         1.02        12.03        15.02        12.66        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-A6EV TCGA-D7-A6EX 
       18.84        18.54        13.35        15.98        11.24        11.31 
TCGA-D7-A6F2 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-8099 TCGA-HJ-7597 TCGA-HU-A4GD 
       15.65        16.24        11.38        17.06        26.47        22.75 
TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP 
       11.77         6.25        12.95        27.42         5.19         6.44 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-MX-A663 TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N5 
        5.56         1.81         9.86         6.08        16.67        57.44 
TCGA-VQ-A8DU TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A925 
        5.46        27.35        14.33        20.81         9.04         4.54 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       54.12        16.14         0.79 

$`6P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30        17.03         0.79        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
        3.68        41.52        42.77        25.41        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE 
       25.22        24.03         6.28        30.25         0.30        24.00 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.48        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
        8.71        13.41        27.12        46.09        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.66         0.10        13.15        15.35         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV 
       11.54        12.33        13.22         4.47        12.33        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.00        12.23        12.03         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       29.59         6.35        53.95         9.30        15.78         2.89 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        7.00        20.38         5.29         4.80        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY 
       18.81        19.96         1.55        18.31        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       10.16         2.10        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        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-7717 TCGA-BR-7722 
       24.76        35.24        23.93        15.42        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-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-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-5799 
       20.42        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-8531 TCGA-CD-8533 
        0.07         0.07         0.10         0.13         0.10         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-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-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
       21.07         7.99        12.36        11.93        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       17.85        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-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-A6EY 
        5.92        15.16        13.78        14.76        13.71        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76         2.96         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-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-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-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-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51        10.19         0.26         2.10        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-A6RN TCGA-IN-A6RO 
       18.81         3.39        18.38         5.36        13.08         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74        12.59         6.51         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-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-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        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-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-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-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-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-AA6G TCGA-VQ-AA6J 
       28.41        32.94        29.98        17.13        26.04        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              0.1               0.0 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            83.24            122.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            12.66             12.79 
[1] "0.1 - 83.2 (12.7)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         2        2        5        2        15        13
  6P LOSS WILD-TYPE       9       17       43       30        62        71
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           6         17          9          5        4
  6P LOSS WILD-TYPE        23         80         63         43       47
                   vv
clus                STAGE IVA
  6P LOSS MUTATED           0
  6P LOSS WILD-TYPE         4
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  2                 9
  STAGE IA                 2                17
  STAGE IB                 5                43
  STAGE II                 2                30
  STAGE IIA               15                62
  STAGE IIB               13                71
  STAGE III                6                23
  STAGE IIIA              17                80
  STAGE IIIB               9                63
  STAGE IIIC               5                43
  STAGE IV                 4                47
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6P LOSS MUTATED       6  17  51  10
  6P LOSS WILD-TYPE    47 109 229 114
D52V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               6                47
  T2                 17               109
  T3                 51               229
  T4                 10               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
  6P LOSS MUTATED    33  24  15  10
  6P LOSS WILD-TYPE 167 158  81  87
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              33               167
  N1              24               158
  N2              15                81
  N3              10                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"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    72   2
  6P LOSS WILD-TYPE 441  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     72    2
  6P LOSS WILD-TYPE  441   37
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              72               441
  1               2                37
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    22  68
  6P LOSS WILD-TYPE 160 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     22   68
  6P LOSS WILD-TYPE  160  359
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              22               160
  MALE                68               359
[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                                                       23
  6P LOSS WILD-TYPE                                                    139
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                                   4
  6P LOSS WILD-TYPE                                                                77
                   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)                         23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  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)                          139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                77
  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  90
  6P LOSS WILD-TYPE   6 513
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   90
  6P LOSS WILD-TYPE    6  513
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0                 6
  YES              90               513
[1] 2 2
[1] FALSE
D52V10, continuous
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    45   0   2   4
  6P LOSS WILD-TYPE 302  18  17  21
D52V11, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              45               302
  R1               0                18
  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"
D52V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED      22                         2
  6P LOSS WILD-TYPE   107                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           0    58
  6P LOSS WILD-TYPE                                         1   327
D52V13, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                                  22               107
  BLACK OR AFRICAN AMERICAN                               2                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  58               327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  60
  6P LOSS WILD-TYPE   6 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   60
  6P LOSS WILD-TYPE    6  334
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              60               334
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    61  41
  6Q LOSS WILD-TYPE 293 180
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              102               473 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               41               180 
$`6Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-JY-A93E 
       25.78        33.27        20.09         4.67        42.77        25.22 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.16         8.94         3.16         0.36        16.47        13.55 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       13.41        83.24        52.57         5.92        12.43        13.41 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 
       13.25        12.59        12.49        22.39        13.22        25.25 
TCGA-R6-A6XG TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC 
       29.59         1.45        12.69        20.02        20.38         3.42 
TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
        9.27        22.82        12.43         8.12        28.11        18.18 
TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7716 
        3.42        19.73         6.18        17.29         9.17        28.01 
TCGA-BR-7722 TCGA-BR-8080 TCGA-BR-A4CQ TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
       15.32         9.60        22.26        13.51        20.65         1.15 
TCGA-CD-5803 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A48A TCGA-CG-4443 
        0.07         0.16         0.10         0.13        12.43        29.98 
TCGA-CG-4455 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6519 
       12.03         1.02        12.03        15.02        12.66        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8576 
       18.84        18.54        13.35        15.98        24.72        14.66 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-A72C 
       11.24        11.31        15.65         7.40        16.24        11.38 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GU 
       17.06        13.58         0.56        26.47        22.75         6.25 
TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU 
       23.84        27.42         5.19         6.44         5.56         1.81 
TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 
        9.86        18.21         6.08        16.67       122.30        57.44 
TCGA-VQ-A8DU TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A922 
        5.46        13.35        27.35        14.33        20.81         9.04 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-ZQ-A9CR 
        2.01         4.54        21.04        54.12        16.14         0.79 

$`6Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02         3.68        41.52        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        24.03         6.28        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        4.31        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL 
       55.50         2.66        35.97        12.92        13.48        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NW 
        7.76         5.49        21.37         8.71        27.12        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.36        10.45        12.66         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.10         0.10        12.46        12.76        12.59         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV 
       15.52        11.54        12.33         4.47        12.33        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       12.00        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        7.00         5.29         4.80        15.35         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
       19.96         1.55        18.31        30.71        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE 
       15.06        11.24         9.17        15.91        10.16         2.10 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         9.57         6.61        34.68        15.95        13.87 
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-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       23.93        15.42        18.15        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-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        12.26        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-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-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-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        19.36         0.46        20.42        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-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-8531 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-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-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-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
       21.07         7.99        12.36        11.93        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       17.85        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-D7-8578 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-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-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 TCGA-ZA-A8F6 
       17.13        26.04        21.11        12.43        10.62 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.00 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            122.3             122.1 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            13.41             12.59 
[1] "0.1 - 122.3 (13.4)" "0.0 - 122.1 (12.6)"
[1] "hr=" "1"  
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         0        2        6        4        15        17
  6Q LOSS WILD-TYPE      11       17       42       28        62        67
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           6         22         11          8        4
  6Q LOSS WILD-TYPE        23         75         61         40       47
                   vv
clus                STAGE IVA
  6Q LOSS MUTATED           1
  6Q LOSS WILD-TYPE         3
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  0                11
  STAGE IA                 2                17
  STAGE IB                 6                42
  STAGE II                 4                28
  STAGE IIA               15                62
  STAGE IIB               17                67
  STAGE III                6                23
  STAGE IIIA              22                75
  STAGE IIIB              11                61
  STAGE IIIC               8                40
  STAGE IV                 4                47
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6Q LOSS MUTATED       5  22  60  13
  6Q LOSS WILD-TYPE    48 104 220 111
D53V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1               5                48
  T2                 22               104
  T3                 60               220
  T4                 13               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
  6Q LOSS MUTATED    33  31  20  14
  6Q LOSS WILD-TYPE 167 151  76  83
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              33               167
  N1              31               151
  N2              20                76
  N3              14                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"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    85   3
  6Q LOSS WILD-TYPE 428  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     85    3
  6Q LOSS WILD-TYPE  428   36
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              85               428
  1               3                36
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    25  82
  6Q LOSS WILD-TYPE 157 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     25   82
  6Q LOSS WILD-TYPE  157  345
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              25               157
  MALE                82               345
[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                                                       27
  6Q LOSS WILD-TYPE                                                    135
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                                   9
  6Q LOSS WILD-TYPE                                                                72
                   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)                         27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               9
  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)                          135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                72
  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     0 107
  6Q LOSS WILD-TYPE   6 496
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0  107
  6Q LOSS WILD-TYPE    6  496
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0                 6
  YES             107               496
[1] 2 2
[1] FALSE
D53V10, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    58   1   2   4
  6Q LOSS WILD-TYPE 289  17  17  21
D53V11, 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"
D53V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED      22                         3
  6Q LOSS WILD-TYPE   107                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           0    70
  6Q LOSS WILD-TYPE                                         1   315
D53V13, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                                  22               107
  BLACK OR AFRICAN AMERICAN                               3                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  70               315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  71
  6Q LOSS WILD-TYPE   6 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   71
  6Q LOSS WILD-TYPE    6  323
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              71               323
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    20  12
  7P LOSS WILD-TYPE 334 209
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               32               543 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               12               209 
$`7P LOSS MUTATED`
TCGA-2H-A9GI TCGA-IG-A3Y9 TCGA-JY-A6FD TCGA-L5-A4OM TCGA-L5-A4OU TCGA-L5-A8NE 
       14.30         0.85        68.02        47.93        29.00        55.50 
TCGA-L5-A8NI TCGA-L5-A8NS TCGA-LN-A49L TCGA-LN-A4A8 TCGA-LN-A7HY TCGA-Q9-A6FU 
       13.48        13.41        10.45        15.52        12.03         5.16 
TCGA-VR-A8EO TCGA-BR-7723 TCGA-BR-8678 TCGA-CD-8528 TCGA-CG-4438 TCGA-CG-4443 
       18.81        28.73        11.54         0.10        54.08        29.98 
TCGA-D7-6820 TCGA-D7-A6EX TCGA-FP-8631 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H6 
       11.31        11.31         0.56        11.77         6.25         9.67 
TCGA-IN-A7NU TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        1.81        37.91        35.61         5.46        13.02        18.48 
TCGA-VQ-A8PJ TCGA-VQ-A91S 
        2.70        22.68 

$`7P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        60.39         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
        6.28         3.16        30.25         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       25.12         0.36         7.40         3.95         3.02         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36         5.92        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        10.52        12.00        12.23        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        2.89         1.45        12.69         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        10.16         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-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-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-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-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-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-8525 
       13.15        13.18         0.30         0.07         0.07         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-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-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        8.05         4.01        14.01        47.05        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-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-D7-5579 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-D7-6817 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-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-A6F0 
       14.76        13.71        11.24        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-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-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-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-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51         5.56         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-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-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79        13.25        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-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        20.81         1.71        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-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-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 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              0.1               0.0 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            68.02            122.30 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           13.215            12.760 
[1] "0.1 - 68.0 (13.2)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0        3        1        1         4         4
  7P LOSS WILD-TYPE      11       16       47       31        73        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           3          8          5          1        3
  7P LOSS WILD-TYPE        26         89         67         47       48
                   vv
clus                STAGE IVA
  7P LOSS MUTATED           0
  7P LOSS WILD-TYPE         4
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                11
  STAGE IA                 3                16
  STAGE IB                 1                47
  STAGE II                 1                31
  STAGE IIA                4                73
  STAGE IIB                4                80
  STAGE III                3                26
  STAGE IIIA               8                89
  STAGE IIIB               5                67
  STAGE IIIC               1                47
  STAGE IV                 3                48
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7P LOSS MUTATED       3   6  18   6
  7P LOSS WILD-TYPE    50 120 262 118
D54V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               3                50
  T2                  6               120
  T3                 18               262
  T4                  6               118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P LOSS MUTATED    12   9   9   3
  7P LOSS WILD-TYPE 188 173  87  94
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              12               188
  N1               9               173
  N2               9                87
  N3               3                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"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    29   2
  7P LOSS WILD-TYPE 484  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     29    2
  7P LOSS WILD-TYPE  484   37
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              29               484
  1               2                37
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     8  25
  7P LOSS WILD-TYPE 174 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8   25
  7P LOSS WILD-TYPE  174  402
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               8               174
  MALE                25               402
[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  33
  7P LOSS WILD-TYPE   6 570
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   33
  7P LOSS WILD-TYPE    6  570
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                 6
  YES              33               570
[1] 2 2
[1] FALSE
D54V10, continuous
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    17   0   2   1
  7P LOSS WILD-TYPE 330  18  17  24
D54V11, 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"
D54V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED       9                         3
  7P LOSS WILD-TYPE   120                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           0    17
  7P LOSS WILD-TYPE                                         1   368
D54V13, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                                   9               120
  BLACK OR AFRICAN AMERICAN                               3                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  17               368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  18
  7P LOSS WILD-TYPE   7 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   18
  7P LOSS WILD-TYPE    7  376
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              18               376
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    30  18
  7Q LOSS WILD-TYPE 324 203
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               48               527 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               18               203 
$`7Q LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A5B8 TCGA-JY-A6FD TCGA-L5-A4OU 
       14.30         5.92         0.85         0.79        68.02        29.00 
TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49L 
       55.50        13.48        13.55         8.71        13.41        10.45 
TCGA-LN-A49X TCGA-LN-A4MR TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-V5-AASX 
        0.10        13.22        12.03        33.11         5.06         4.44 
TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-AA7I TCGA-BR-7723 TCGA-BR-8369 TCGA-BR-8678 
       18.81         1.55        15.91        28.73        14.04        11.54 
TCGA-BR-A4CS TCGA-CD-8528 TCGA-CD-A48C TCGA-CG-4438 TCGA-CG-4443 TCGA-D7-6820 
        1.48         0.10        11.61        54.08        29.98        11.31 
TCGA-D7-8575 TCGA-D7-A6EX TCGA-FP-7829 TCGA-FP-8631 TCGA-HU-A4GD TCGA-HU-A4GH 
       18.21        11.31        19.53         0.56        22.75        11.77 
TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A7NU TCGA-KB-A93H 
        6.25         9.67        27.42        18.38         1.81        37.64 
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 

$`7Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       16.24         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       30.25         0.30         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.95         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        16.47        13.22         7.76         5.49        21.37 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.25        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18         0.13         5.16         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        22.82        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        10.16         3.42         2.10         2.66        19.73 
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-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-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        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-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
        7.99         8.05         4.01        14.01        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-D7-6521 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-D7-6822 
       10.26        15.22        15.98        12.79        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        13.71        11.24        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-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-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         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-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-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        23.84        12.30         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39         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-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 
              0.1               0.0 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            68.02            122.30 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.12             12.76 
[1] "0.1 - 68.0 (13.1)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         1        2        2        2         9         8
  7Q LOSS WILD-TYPE      10       17       46       30        68        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           6         10          4          2        3
  7Q LOSS WILD-TYPE        23         87         68         46       48
                   vv
clus                STAGE IVA
  7Q LOSS MUTATED           0
  7Q LOSS WILD-TYPE         4
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1                10
  STAGE IA                 2                17
  STAGE IB                 2                46
  STAGE II                 2                30
  STAGE IIA                9                68
  STAGE IIB                8                76
  STAGE III                6                23
  STAGE IIIA              10                87
  STAGE IIIB               4                68
  STAGE IIIC               2                46
  STAGE IV                 3                48
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7Q LOSS MUTATED       3   7  32   7
  7Q LOSS WILD-TYPE    50 119 248 117
D55V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               3                50
  T2                  7               119
  T3                 32               248
  T4                  7               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
  7Q LOSS MUTATED    20  14  10   5
  7Q LOSS WILD-TYPE 180 168  86  92
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              20               180
  N1              14               168
  N2              10                86
  N3               5                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"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    46   2
  7Q LOSS WILD-TYPE 467  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     46    2
  7Q LOSS WILD-TYPE  467   37
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              46               467
  1               2                37
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    11  40
  7Q LOSS WILD-TYPE 171 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11   40
  7Q LOSS WILD-TYPE  171  387
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              11               171
  MALE                40               387
[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  51
  7Q LOSS WILD-TYPE   6 552
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   51
  7Q LOSS WILD-TYPE    6  552
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                 6
  YES              51               552
[1] 2 2
[1] FALSE
D55V10, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    26   0   2   1
  7Q LOSS WILD-TYPE 321  18  17  24
D55V11, 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"
D55V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED      15                         2
  7Q LOSS WILD-TYPE   114                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           0    27
  7Q LOSS WILD-TYPE                                         1   358
D55V13, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                                  15               114
  BLACK OR AFRICAN AMERICAN                               2                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  27               358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  31
  7Q LOSS WILD-TYPE   7 363
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   31
  7Q LOSS WILD-TYPE    7  363
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              31               363
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    83  58
  8P LOSS WILD-TYPE 271 163
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              141               434 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               163 
$`8P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB 
       25.78         5.92        13.94         7.69         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12         3.88         0.53         0.79        23.41         9.96 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E 
       14.50        44.75        60.39        25.41        23.18        25.22 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO 
        8.94        24.00         3.68        32.61        21.01         3.32 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NR 
        7.40         3.95        55.50         2.66         5.49         8.71 
TCGA-L5-A8NT TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A1 
       27.12        10.45        12.66        12.43        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW 
       12.49        22.39        12.33        13.22        12.33        12.00 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB 
        5.16         7.82         8.02         1.45        20.38         5.29 
TCGA-V5-A7RC TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        3.42        12.43        18.31        42.87        15.06         9.17 
TCGA-VR-AA7I TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6456 
       15.91         2.66        19.56         9.44        18.35        17.29 
TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8077 
       25.61        12.16        28.01        28.73        12.76         0.69 
TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
       12.95        15.58        13.08        15.81        16.44         9.86 
TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF 
        8.22        13.87        12.89         0.72        13.51         1.15 
TCGA-BR-A4QI TCGA-CD-8526 TCGA-CD-8533 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 
       13.64         0.07         0.13        11.61        12.20         3.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4475 TCGA-CG-5724 
        7.99        54.08         4.01        19.07        22.98        12.03 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 
        4.01        69.04        18.54        10.26        15.22        11.31 
TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       24.72        18.21        16.44        15.65         7.40         0.62 
TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GU TCGA-HU-A4HD 
       17.06         5.92        14.17         0.76         6.25        27.42 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 
        1.41         6.44         6.74         1.81         7.82         2.53 
TCGA-KB-A6F5 TCGA-R5-A7O7 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW 
        5.56        45.67         9.24         8.61       122.30        37.91 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PK 
       18.48        35.24        34.45         7.73        46.26        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A925 
        1.87        13.35        20.81         1.71        52.24         4.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       11.24        18.41        40.08        29.98        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       21.11        12.43         0.79 

$`8P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        14.30        58.55         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         6.21        33.27        20.09        20.78 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       18.64         9.30        17.03        12.82        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        68.02         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30         4.31         4.70        19.99        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        0.36         3.02        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55        13.22         7.76        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R 
       52.57        46.09        10.36         5.92        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 
       13.15        15.35         0.10        13.25         0.10        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59         0.10        15.52        11.54         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.23        12.03        13.18         0.13        33.11 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.02         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96        22.82         1.55         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.18        46.19        11.24        10.16         3.42         2.10 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
       19.73        26.70        11.70        11.01         9.47         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-6706 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        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-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       15.32        12.43         3.45         9.07        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-8295 TCGA-BR-8297 TCGA-BR-8360 
        0.56         2.66        16.31         2.20         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-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-8686 TCGA-BR-8690 
        6.28         7.53         0.49        11.54        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-D7-6822 
       13.35        17.19        15.98        12.79        10.55        12.33 
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-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-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44         9.76         2.96         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         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-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-8245 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        12.59        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-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-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-A6RS TCGA-IN-A7NR 
       18.38         5.36         5.19        13.08        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
        5.56        13.51        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73         9.86        18.21         8.52        61.25         6.08 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.60        11.05         5.13        16.67        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-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       13.02        21.73        27.88        32.48        28.96        34.29 
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-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-A91Y TCGA-VQ-A922 
       22.68        36.16         7.36         9.50         9.73         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-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
        2.66        42.54        22.09        28.41        32.94        17.13 
TCGA-VQ-AA6G TCGA-ZA-A8F6 
       26.04        10.62 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.07              0.00 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            122.3             122.1 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           12.490            12.805 
[1] "0.1 - 122.3 (12.5)" "0.0 - 122.1 (12.8)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         4        3        5        4        15        22
  8P LOSS WILD-TYPE       7       16       43       28        62        62
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           7         24         26         13       14
  8P LOSS WILD-TYPE        22         73         46         35       37
                   vv
clus                STAGE IVA
  8P LOSS MUTATED           1
  8P LOSS WILD-TYPE         3
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  4                 7
  STAGE IA                 3                16
  STAGE IB                 5                43
  STAGE II                 4                28
  STAGE IIA               15                62
  STAGE IIB               22                62
  STAGE III                7                22
  STAGE IIIA              24                73
  STAGE IIIB              26                46
  STAGE IIIC              13                35
  STAGE IV                14                37
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8P LOSS MUTATED      15  23  78  26
  8P LOSS WILD-TYPE    38 103 202  98
D56V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              15                38
  T2                 23               103
  T3                 78               202
  T4                 26                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P LOSS MUTATED    35  48  30  27
  8P LOSS WILD-TYPE 165 134  66  70
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              35               165
  N1              48               134
  N2              30                66
  N3              27                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"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   124  10
  8P LOSS WILD-TYPE 389  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    124   10
  8P LOSS WILD-TYPE  389   29
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             124               389
  1              10                29
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    29 117
  8P LOSS WILD-TYPE 153 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     29  117
  8P LOSS WILD-TYPE  153  310
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              29               153
  MALE               117               310
[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                                                       32
  8P LOSS WILD-TYPE                                                    130
                   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                                                 22
  8P LOSS WILD-TYPE                                               56
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8P LOSS MUTATED                                                          2
  8P LOSS WILD-TYPE                                                       19
                   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)                         32
  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                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  8P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  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                         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     1 145
  8P LOSS WILD-TYPE   5 458
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1  145
  8P LOSS WILD-TYPE    5  458
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                1                 5
  YES             145               458
[1] 2 2
[1] FALSE
D56V10, continuous
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED    70   4   7   2
  8P LOSS WILD-TYPE 277  14  12  23
D56V11, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              70               277
  R1               4                14
  R2               7                12
  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"
D56V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED      33                         4
  8P LOSS WILD-TYPE    96                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           1    87
  8P LOSS WILD-TYPE                                         0   298
D56V13, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                                  33                96
  BLACK OR AFRICAN AMERICAN                               4                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  87               298
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     2  86
  8P LOSS WILD-TYPE   5 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2   86
  8P LOSS WILD-TYPE    5  308
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              86               308
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    33  22
  8Q LOSS WILD-TYPE 321 199
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               55               520 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               199 
$`8Q LOSS MUTATED`
TCGA-2H-A9GL TCGA-IG-A5S3 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A93E TCGA-L5-A43M 
        5.92        23.41        44.75        60.39        25.22         8.94 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        3.68        32.61        21.01         3.95        55.50         2.66 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A7HW 
       10.45        12.43        12.46        12.33        13.22        12.00 
TCGA-V5-A7RC TCGA-VR-A8Q7 TCGA-Z6-AAPN TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6705 
        3.42        42.87         2.66         9.44        18.35        25.61 
TCGA-BR-8286 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4440 
       12.95        13.51        13.64        11.61        12.20         4.01 
TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 TCGA-FP-8099 
       12.03        18.54        10.26        15.22        24.72        17.06 
TCGA-HU-8249 TCGA-IN-A7NU TCGA-IN-AB1V TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV 
       14.17         1.81         7.82         9.24         8.61       122.30 
TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A91U 
       18.48        34.45        17.85         1.87        14.33         1.71 
TCGA-VQ-A925 TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
        4.54        11.24        29.98        54.12        16.14        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`8Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
      122.10        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       30.25         0.30         4.31        24.00         4.70        19.99 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
        8.71         2.60        25.12         0.36         7.40         3.02 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       83.24        52.57        46.09        10.36         5.92        12.66 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10        15.52        11.54         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        2.89         1.45        12.69         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        30.71        18.18        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        9.17        15.91        10.16         3.42         2.10        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.47         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-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-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-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-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-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-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-A487 
        0.10         0.13         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-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-4449 TCGA-CG-4455 
       54.08        14.01        29.98        47.05        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-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-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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85        13.35        17.19        15.98        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-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-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-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-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-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-8663 TCGA-IN-A6RI 
       27.42        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-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         6.51         5.56        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-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-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-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        35.24        21.73        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-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       12.79         2.70         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       26.24        27.35        64.57        65.16        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-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-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-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-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        26.04        12.43        10.62 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.79              0.00 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            122.3             122.1 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            12.95             12.76 
[1] "0.8 - 122.3 (12.9)" "0.0 - 122.1 (12.8)"
[1] "hr=" "1"  
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         3        1        1        2         8         8
  8Q LOSS WILD-TYPE       8       18       47       30        69        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           2          8         10          2        5
  8Q LOSS WILD-TYPE        27         89         62         46       46
                   vv
clus                STAGE IVA
  8Q LOSS MUTATED           1
  8Q LOSS WILD-TYPE         3
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  3                 8
  STAGE IA                 1                18
  STAGE IB                 1                47
  STAGE II                 2                30
  STAGE IIA                8                69
  STAGE IIB                8                76
  STAGE III                2                27
  STAGE IIIA               8                89
  STAGE IIIB              10                62
  STAGE IIIC               2                46
  STAGE IV                 5                46
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8Q LOSS MUTATED       6  10  34   4
  8Q LOSS WILD-TYPE    47 116 246 120
D57V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               6                47
  T2                 10               116
  T3                 34               246
  T4                  4               120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q LOSS MUTATED    16  15  11  11
  8Q LOSS WILD-TYPE 184 167  85  86
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              16               184
  N1              15               167
  N2              11                85
  N3              11                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"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    47   4
  8Q LOSS WILD-TYPE 466  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     47    4
  8Q LOSS WILD-TYPE  466   35
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              47               466
  1               4                35
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    12  44
  8Q LOSS WILD-TYPE 170 383
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     12   44
  8Q LOSS WILD-TYPE  170  383
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              12               170
  MALE                44               383
[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                                                       11
  8Q LOSS WILD-TYPE                                                    151
                   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                                                  8
  8Q LOSS WILD-TYPE                                               70
                   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)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                8
  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)                          151
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                70
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 70
  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  56
  8Q LOSS WILD-TYPE   6 547
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   56
  8Q LOSS WILD-TYPE    6  547
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 6
  YES              56               547
[1] 2 2
[1] FALSE
D57V10, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    25   0   4   2
  8Q LOSS WILD-TYPE 322  18  15  23
D57V11, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              25               322
  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"
D57V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED      11                         3
  8Q LOSS WILD-TYPE   118                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           1    36
  8Q LOSS WILD-TYPE                                         0   349
D57V13, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                                  11               118
  BLACK OR AFRICAN AMERICAN                               3                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  36               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  30
  8Q LOSS WILD-TYPE   7 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   30
  8Q LOSS WILD-TYPE    7  364
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              30               364
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   140  90
  9P LOSS WILD-TYPE 214 131
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              230               345 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               90               131 
$`9P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        7.69        20.78        20.12        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
        0.79        23.41         9.96         4.67        14.50        12.16 
TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OF 
       60.39        25.41        25.22         3.16         8.94         3.68 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW 
       32.61        47.93        18.35         7.17        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.43         6.94         2.60         3.95        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       35.97        16.47        13.22         8.71        13.41        83.24 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43         0.10        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       22.39         0.10        15.52        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        10.52        12.00        12.23        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
       33.11         5.16         5.06        29.59         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         1.45        12.69        20.02         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
        4.80         9.27         4.44        18.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55        18.31         8.12        28.11        42.87        46.19 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 
       10.16         3.42        19.73        11.01         9.44        18.35 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7716 
       13.68        19.33        31.20         9.21        35.24        28.01 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
       18.15        28.73         3.45        18.71        17.49        11.44 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 
        0.69        12.95        16.31        22.19        17.52        14.04 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-8686 
        5.39        25.18         9.21        20.22         9.86        15.68 
TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 
        8.22        13.87        22.26         1.48         0.72         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 
       13.51        20.65         1.15         3.25        13.15         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 
        3.42        11.61         3.02        54.08         4.01        19.07 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 
       12.03        18.97        12.00        36.00         1.02        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
        4.01        69.04        12.66        11.93        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.54        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 
       14.66        21.14        16.44        11.24        11.31         2.96 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8631 
        7.40         7.99        72.23        11.38        17.06         0.56 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H6 
        1.51         5.92        12.59        11.77         6.25         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RR 
       27.42        21.21        18.81         5.36         1.41         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF 
        6.51         5.56         7.82        37.64        45.67         8.52 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        6.08         9.24         8.61         5.13        16.67        37.91 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        8.94         5.79        13.25        18.48        35.24        34.45 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
        7.73        22.19        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       27.35        64.57        14.33        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
       36.16         9.50         9.73        21.04        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J 
       22.09        18.41        40.08        32.94        54.12        21.11 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`9P LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IC-A6RF 
       58.55         7.63         5.92        13.94        32.45         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D 
       33.27        20.09         0.85         2.63         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       12.82        14.86       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       41.52        42.77        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
        6.28        30.25         0.30         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
       19.99        21.01         3.32         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
       29.00         8.71        25.12         0.36         7.40         3.02 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.48        13.55         7.76         5.49        21.37 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O 
       27.12        52.57        46.09        10.36         5.92        13.41 
TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HY TCGA-Q9-A6FW 
        0.10        12.59        11.54         4.47        12.03         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 
        8.02         7.59        14.70         7.04        53.95         2.89 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EY TCGA-VR-A8EZ 
        7.00        20.38        15.35        19.96        30.71        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.06        11.24         9.17        15.91         2.10         2.66 
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-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       23.93        15.42        15.32        12.43         9.07        12.76 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        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-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       13.08         0.26         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-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-8690 
        7.53         0.49        11.54        15.81        16.44        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56         7.53         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-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
       20.42        13.64        11.57         5.13         2.83        13.18 
TCGA-CD-5802 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 
        0.30         0.10         0.13         0.16         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10         9.34        11.31        12.43         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4460 
        7.99         8.05        14.01        29.98        47.05        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        22.98        30.97         6.97 
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-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 
       79.07        65.10        21.07         7.99        12.36        19.13 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       18.61        17.85        15.22        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 
       24.72        16.80        19.50        17.19        18.21        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-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
        8.81         3.45         3.39        18.38         5.19        13.08 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.44        12.59         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-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
       61.25         4.60        11.05       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-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92        48.79         5.46        13.02        21.73        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       32.48        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ 
        9.27        23.41        15.65        13.35        26.24        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-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        10.62 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.00 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            83.24            122.30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            12.59             12.89 
[1] "0.1 - 83.2 (12.6)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         2        8       14       16        32        35
  9P LOSS WILD-TYPE       9       11       34       16        45        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED          16         35         28         13       20
  9P LOSS WILD-TYPE        13         62         44         35       31
                   vv
clus                STAGE IVA
  9P LOSS MUTATED           4
  9P LOSS WILD-TYPE         0
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  2                 9
  STAGE IA                 8                11
  STAGE IB                14                34
  STAGE II                16                16
  STAGE IIA               32                45
  STAGE IIB               35                49
  STAGE III               16                13
  STAGE IIIA              35                62
  STAGE IIIB              28                44
  STAGE IIIC              13                35
  STAGE IV                20                31
  STAGE IVA                4                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9P LOSS MUTATED      21  53 114  39
  9P LOSS WILD-TYPE    32  73 166  85
D58V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              21                32
  T2                 53                73
  T3                114               166
  T4                 39                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"
                   vv
clus                 N0  N1  N2  N3
  9P LOSS MUTATED    74  81  41  29
  9P LOSS WILD-TYPE 126 101  55  68
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              74               126
  N1              81               101
  N2              41                55
  N3              29                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"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   201  14
  9P LOSS WILD-TYPE 312  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    201   14
  9P LOSS WILD-TYPE  312   25
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             201               312
  1              14                25
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    64 177
  9P LOSS WILD-TYPE 118 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     64  177
  9P LOSS WILD-TYPE  118  250
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              64               118
  MALE               177               250
[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                                                                  36
  9P LOSS WILD-TYPE                                                                45
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  9P LOSS MUTATED                                                 32
  9P LOSS WILD-TYPE                                               46
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9P LOSS MUTATED                                                          7
  9P LOSS WILD-TYPE                                                       14
                   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)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        7
  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)                45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 46
  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"
D58V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     3 238
  9P LOSS WILD-TYPE   3 365
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3  238
  9P LOSS WILD-TYPE    3  365
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                3                 3
  YES             238               365
[1] 2 2
[1] FALSE
D58V10, continuous
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED   120   5   6   5
  9P LOSS WILD-TYPE 227  13  13  20
D58V11, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             120               227
  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"
D58V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED      56                         7
  9P LOSS WILD-TYPE    73                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           1   143
  9P LOSS WILD-TYPE                                         0   242
D58V13, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                                  56                73
  BLACK OR AFRICAN AMERICAN                               7                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 143               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"
D58V14, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     4 151
  9P LOSS WILD-TYPE   3 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  151
  9P LOSS WILD-TYPE    3  243
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             151               243
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    96  63
  9Q LOSS WILD-TYPE 258 158
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              159               416 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               63               158 
$`9Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YA 
       25.78        31.27        16.24         4.21         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12        18.64         3.88         0.79        23.41         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OM 
        4.67        14.50        25.22         8.94         3.68        47.93 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NF 
       58.59         7.13         6.94         2.60        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
       35.97        13.22        13.41        83.24        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.43         0.10        13.15        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.76         0.10        12.33        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
       13.18         0.13         5.06        29.59         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO 
       15.78        12.69         5.29         3.42         4.80        18.81 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
        1.55         8.12        28.11        42.87        46.19        11.24 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-BR-6457 
       10.16         3.42         2.10        19.73        11.01        13.68 
TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 
       19.33        31.20         9.21        28.01        28.73         3.45 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 
       17.49        11.44        12.95        16.31        22.19        17.52 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8686 TCGA-BR-A44U TCGA-BR-A4CQ 
        5.39        25.18         9.21        15.68        13.87        22.26 
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-4455 
       11.61        12.20         3.02        54.08         4.01        12.03 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
       20.55        18.84        18.54        13.35        10.26        15.98 
TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6F0 
       12.79        18.21        14.66        21.14        16.44         2.96 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 
        7.40         7.99        72.23        11.38        17.06        13.58 
TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4HD 
        0.56         5.92        11.77         6.25         2.10        27.42 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93H 
       18.38         5.36         6.74         6.51         7.82        37.64 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 
       45.67         8.52         6.08        16.67        37.91         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PE 
        5.79        13.25        18.48        35.24        34.45        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A91Q 
       12.79         2.70        17.85        13.35        64.57        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-AA6F TCGA-VQ-AA6J 
       32.94        54.12        21.11 

$`9Q LOSS WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB 
       32.45         7.69         6.21        33.27        20.09         2.63 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97I 
        9.30         0.53        17.03        12.82        14.86        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       42.77        25.41        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
        6.28         3.16        30.25         0.30         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        4.70        32.61        19.99        21.01        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         1.38         3.16         4.90        29.00         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37         8.71        27.12        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        5.92        13.41        15.35         0.10        13.25         0.10 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        4.47        25.25        12.03        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 
        8.02         7.59        14.70         7.04        53.95         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASW 
        1.45         7.00        20.02        20.38        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY 
        4.44        19.96        22.82        12.43        18.31        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-AAPN TCGA-B7-5816 
       18.18        15.06         9.17        15.91         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56         9.47         9.44         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-6455 TCGA-BR-6456 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        17.29        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-6852 TCGA-BR-7196 
       12.16         8.98        21.11        30.90        32.94        12.82 
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-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 
       12.43         9.07        12.76        18.71        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
       12.26         9.60        20.55         8.05         0.56         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-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        0.26         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-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-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
        9.86         8.22        10.68        12.56         7.53         6.08 
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-A4PD TCGA-BR-A4PE 
       12.82         0.66        19.36         0.46        20.65        20.42 
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-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.30         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
        0.13         0.10         9.34        11.31        12.43         6.58 
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-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        7.99         8.05        14.01        29.98        47.05        19.07 
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-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-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        11.93        19.13        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       17.19        15.22        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       16.80        19.50        17.19        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-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-A4BF TCGA-FP-A8CX 
       14.07        22.29        59.54         5.03         5.52         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       18.08        26.47         1.51        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-A4GX 
       21.37        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26        12.95        19.36        23.84        12.30         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-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT 
        5.19        13.08         1.41         6.44        12.59         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-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 
        3.72        19.73         9.86        18.21        61.25         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        9.24        11.05         8.61         5.13       122.30        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-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 
       19.04         0.92        48.79         5.46        13.02        21.73 
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-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       26.24        27.35        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        18.74        22.68        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50        52.24         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58         5.72        64.18         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       28.41        29.98        17.13        26.04        16.14        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            83.24            122.30 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            12.66             12.82 
[1] "0.1 - 83.2 (12.7)"  "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        5       11       12        22        26
  9Q LOSS WILD-TYPE      10       14       37       20        55        58
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           8         26         19         11       12
  9Q LOSS WILD-TYPE        21         71         53         37       39
                   vv
clus                STAGE IVA
  9Q LOSS MUTATED           4
  9Q LOSS WILD-TYPE         0
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  1                10
  STAGE IA                 5                14
  STAGE IB                11                37
  STAGE II                12                20
  STAGE IIA               22                55
  STAGE IIB               26                58
  STAGE III                8                21
  STAGE IIIA              26                71
  STAGE IIIB              19                53
  STAGE IIIC              11                37
  STAGE IV                12                39
  STAGE IVA                4                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9Q LOSS MUTATED      14  37  83  26
  9Q LOSS WILD-TYPE    39  89 197  98
D59V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              14                39
  T2                 37                89
  T3                 83               197
  T4                 26                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 LOSS MUTATED    53  55  26  24
  9Q LOSS WILD-TYPE 147 127  70  73
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              53               147
  N1              55               127
  N2              26                70
  N3              24                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"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   138  12
  9Q LOSS WILD-TYPE 375  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    138   12
  9Q LOSS WILD-TYPE  375   27
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             138               375
  1              12                27
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    40 129
  9Q LOSS WILD-TYPE 142 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     40  129
  9Q LOSS WILD-TYPE  142  298
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              40               142
  MALE               129               298
[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                                                       41
  9Q LOSS WILD-TYPE                                                    121
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                                  24
  9Q LOSS WILD-TYPE                                                                57
                   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)                         41
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              24
  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)                          121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                57
  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     3 166
  9Q LOSS WILD-TYPE   3 437
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3  166
  9Q LOSS WILD-TYPE    3  437
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                3                 3
  YES             166               437
[1] 2 2
[1] FALSE
D59V10, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    84   3   4   4
  9Q LOSS WILD-TYPE 263  15  15  21
D59V11, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              84               263
  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"
D59V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED      41                         7
  9Q LOSS WILD-TYPE    88                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           0   103
  9Q LOSS WILD-TYPE                                         1   282
D59V13, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                                  41                88
  BLACK OR AFRICAN AMERICAN                               7                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 103               282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     4 112
  9Q LOSS WILD-TYPE   3 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4  112
  9Q LOSS WILD-TYPE    3  282
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             112               282
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    57  48
  10P LOSS WILD-TYPE 297 173
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               105                470 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                48                173 
$`10P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A50L 
       25.78        14.30         5.92        33.27         0.85         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43J 
        0.79        23.41        14.50        23.18         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW 
        8.94        24.00         4.70         3.32         4.90         7.13 
TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O 
       13.55        13.41        27.12        83.24        12.66        13.41 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        12.33        13.22         4.47        25.25        12.00 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP 
       13.18         0.13         7.82         3.42         4.80        19.96 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-Z6-A8JD 
        8.12        28.11        18.18        15.06        11.24         3.42 
TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6564 
        2.66        19.56        18.35         6.18        19.33        26.10 
TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8484 
       35.24         3.45        11.44        16.31        17.52        25.18 
TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4IY TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
       20.22         7.53        12.89         0.07         0.07         0.10 
TCGA-CD-8533 TCGA-CG-4455 TCGA-CG-4475 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6527 
        0.13        12.03        22.98        69.04        18.54        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EV TCGA-EQ-8122 
       15.22        15.98        11.31        18.21        11.24         7.99 
TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8249 TCGA-IN-8462 
       19.53         0.56         5.52         0.23        14.17        18.81 
TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-R5-A7O7 
       18.38         1.41         6.44         6.74         6.51        45.67 
TCGA-R5-A7ZF TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DZ 
        8.52       115.69         8.94         5.79        48.79        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91A 
       18.48        35.24        22.19        17.85        13.35        36.69 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 
       18.74        20.81         5.72        21.04        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       40.08        16.14         0.79 

$`10P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         7.69         6.21        20.09        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.16        30.25         3.68        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        0.36         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        5.49        21.37         8.71        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        5.92        10.45        12.43         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
        0.10        13.25         0.10        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U6 
       12.76        12.59        22.39         0.10        15.52        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN 
       10.52        12.23        12.03        33.11         5.16         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.02        20.38         5.29        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        22.82        12.43         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       30.71        42.87        46.19         9.17        15.91        10.16 
TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.10        19.73        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.44         6.61         6.97         4.64         7.43        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-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        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-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-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-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-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72         5.39         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-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-4460 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        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-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-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        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-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-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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       59.54         5.03        13.58        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-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-7806 TCGA-IN-7808 TCGA-IN-8663 
        8.88         8.81        27.42        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-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-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA69 
        6.58        64.18         2.66        42.54        22.09        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       32.94        29.98        17.13        54.12        26.04        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       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 
            13.180             12.675 
[1] "0.1 - 115.7 (13.2)" "0.0 - 122.3 (12.7)"
[1] "hr=" "1.3"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         2        2        4        5        14        19
  10P LOSS WILD-TYPE       9       17       44       27        63        65
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           5         18         14          9       12
  10P LOSS WILD-TYPE        24         79         58         39       39
                    vv
clus                 STAGE IVA
  10P LOSS MUTATED           1
  10P LOSS WILD-TYPE         3
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   2                  9
  STAGE IA                  2                 17
  STAGE IB                  4                 44
  STAGE II                  5                 27
  STAGE IIA                14                 63
  STAGE IIB                19                 65
  STAGE III                 5                 24
  STAGE IIIA               18                 79
  STAGE IIIB               14                 58
  STAGE IIIC                9                 39
  STAGE IV                 12                 39
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10P LOSS MUTATED       7  25  60  14
  10P LOSS WILD-TYPE    46 101 220 110
D60V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1                7                 46
  T2                  25                101
  T3                  60                220
  T4                  14                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
  10P LOSS MUTATED    31  30  23  22
  10P LOSS WILD-TYPE 169 152  73  75
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               31                169
  N1               30                152
  N2               23                 73
  N3               22                 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"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    95   8
  10P LOSS WILD-TYPE 418  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     95    8
  10P LOSS WILD-TYPE  418   31
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               95                418
  1                8                 31
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    30  81
  10P LOSS WILD-TYPE 152 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     30   81
  10P LOSS WILD-TYPE  152  346
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               30                152
  MALE                 81                346
[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                                                       22
  10P LOSS WILD-TYPE                                                    140
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                                  13
  10P LOSS WILD-TYPE                                                                68
                    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)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               13
  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)                           140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 68
  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     1 110
  10P LOSS WILD-TYPE   5 493
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1  110
  10P LOSS WILD-TYPE    5  493
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 1                  5
  YES              110                493
[1] 2 2
[1] FALSE
D60V10, continuous
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    54   3   1   5
  10P LOSS WILD-TYPE 293  15  18  20
D60V11, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               54                293
  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"
D60V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED      24                         5
  10P LOSS WILD-TYPE   105                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           0    68
  10P LOSS WILD-TYPE                                         1   317
D60V13, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                                   24                105
  BLACK OR AFRICAN AMERICAN                                5                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   68                317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  68
  10P LOSS WILD-TYPE   6 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   68
  10P LOSS WILD-TYPE    6  326
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               68                326
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    65  41
  10Q LOSS WILD-TYPE 289 180
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               106                469 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                41                180 
$`10Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB 
       25.78        14.30         5.92        33.27         0.85         2.63 
TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H 
        0.53        23.41        14.50        23.18         3.16         0.30 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NK 
       24.00         4.70         3.32         4.90         7.13        13.55 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 
       27.12        83.24        12.66         0.10        12.46        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       22.39         0.10        11.54        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-V5-A7RC 
       25.25        12.00        12.03        13.18         5.16         3.42 
TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-Z6-A8JE TCGA-Z6-AAPN 
        4.80        19.96        28.11        18.18         2.10         2.66 
TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8060 
       19.56        18.35        19.33        35.24         3.45        11.44 
TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       16.31        17.52         5.39        25.18         9.21        20.22 
TCGA-BR-8683 TCGA-BR-A4CQ TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A48A 
        9.86        22.26         3.25         0.07         0.10        12.43 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5730 
        7.99         4.01        12.03        18.97        22.98         4.01 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       19.13        18.54        10.26        15.22        15.98        12.79 
TCGA-EQ-8122 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 
        7.99         0.56         5.52         0.23         5.92        14.17 
TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RO 
       12.10        11.77        27.42        18.81        18.38         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF 
        6.44         6.74         6.51        37.64        45.67         8.52 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94         5.79        48.79         5.46        13.02        18.48 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A94O 
       22.19        17.85        36.69        18.74         9.50        21.04 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       11.24        40.08        32.94         0.79 

$`10Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         7.69         6.21        20.09        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
       30.25         4.31         8.94         3.68        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       58.59        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36         5.92        10.45        12.43        13.41 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35         0.10        13.25         0.10        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       12.76        12.59        15.52         4.47        10.52        12.23 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.38         5.29        15.35         9.27         4.44        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
       10.16         3.42        19.73        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        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-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        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-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-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        12.95         2.66         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        6.18        19.50        13.08         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 
       14.79         0.26        15.85         3.72         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-A4CS TCGA-BR-A4IU 
       12.56        13.87         7.53         6.08         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-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-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-4437 TCGA-CG-4438 TCGA-CG-4441 
       27.02        15.95         1.02         8.05        54.08        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-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-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-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.36        12.66        11.93        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        13.35        17.19        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-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-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-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       59.54         5.03        13.58        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        12.59        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-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
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-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
        3.45         3.39         5.36         5.19        13.08        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-A7ZE 
       60.56        20.15         3.72        19.73         9.86        18.21 
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-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        13.25        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-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-A91Q TCGA-VQ-A91S 
       65.16        11.70        11.93        61.22        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71        36.16         7.36         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-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        42.54        22.09        18.41        28.41        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 
       10.62 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             83.24             122.30 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             12.38              12.82 
[1] "0.1 - 83.2 (12.4)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         2        3        4        5        17        14
  10Q LOSS WILD-TYPE       9       16       44       27        60        70
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           7         21         11         12        8
  10Q LOSS WILD-TYPE        22         76         61         36       43
                    vv
clus                 STAGE IVA
  10Q LOSS MUTATED           1
  10Q LOSS WILD-TYPE         3
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   2                  9
  STAGE IA                  3                 16
  STAGE IB                  4                 44
  STAGE II                  5                 27
  STAGE IIA                17                 60
  STAGE IIB                14                 70
  STAGE III                 7                 22
  STAGE IIIA               21                 76
  STAGE IIIB               11                 61
  STAGE IIIC               12                 36
  STAGE IV                  8                 43
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10Q LOSS MUTATED       8  26  54  17
  10Q LOSS WILD-TYPE    45 100 226 107
D61V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1                8                 45
  T2                  26                100
  T3                  54                226
  T4                  17                107
[1] 4 2
[1] 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    31  33  19  22
  10Q LOSS WILD-TYPE 169 149  77  75
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               31                169
  N1               33                149
  N2               19                 77
  N3               22                 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"
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    96   8
  10Q LOSS WILD-TYPE 417  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     96    8
  10Q LOSS WILD-TYPE  417   31
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               96                417
  1                8                 31
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    30  81
  10Q LOSS WILD-TYPE 152 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     30   81
  10Q LOSS WILD-TYPE  152  346
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               30                152
  MALE                 81                346
[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                                                       21
  10Q LOSS WILD-TYPE                                                    141
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                                  16
  10Q LOSS WILD-TYPE                                                                65
                    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                                                          4
  10Q LOSS WILD-TYPE                                                       17
                    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)                          21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               16
  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                                                                  10Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 65
  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"
D61V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1 110
  10Q LOSS WILD-TYPE   5 493
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1  110
  10Q LOSS WILD-TYPE    5  493
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 1                  5
  YES              110                493
[1] 2 2
[1] FALSE
D61V10, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    53   2   3   4
  10Q LOSS WILD-TYPE 294  16  16  21
D61V11, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               53                294
  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"
D61V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED      30                         5
  10Q LOSS WILD-TYPE    99                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           0    62
  10Q LOSS WILD-TYPE                                         1   323
D61V13, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                                   30                 99
  BLACK OR AFRICAN AMERICAN                                5                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   62                323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  73
  10Q LOSS WILD-TYPE   6 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   73
  10Q LOSS WILD-TYPE    6  321
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               73                321
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    69  43
  11P LOSS WILD-TYPE 285 178
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               112                463 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                43                178 
$`11P LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YB 
       31.27        14.30         5.92         4.21         0.85         2.63 
TCGA-IG-A5S3 TCGA-JY-A938 TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OG TCGA-L5-A4OO 
       23.41        25.41         3.16         0.30         4.70         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 
        7.17         3.16         6.94         2.60         0.36         3.02 
TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NT TCGA-L7-A6VZ 
       55.50        16.47        13.55        13.22        27.12        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W 
       10.45        12.66        12.43        13.41         0.10        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A7HY 
       12.59        12.49        12.76         0.10        12.33        12.03 
TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC 
        0.13         5.06        29.59         6.35         2.89         1.45 
TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EX 
       12.69         4.80         9.27        18.81        12.43        28.11 
TCGA-Z6-A8JE TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7723 
        2.10         6.61         6.97         9.57        26.10        28.73 
TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-CD-5799 
        9.60         2.66         7.40         1.48         0.72         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4443 
       13.15         0.30         0.07         3.42        12.43        29.98 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5578 
       47.05        21.99        30.97        12.03         4.01        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       11.93        20.55        18.54        10.26        15.22        15.98 
TCGA-D7-8578 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8211 
       21.14         7.40         0.62        72.23        11.38        13.58 
TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H4 
       26.47        12.59        14.17        22.75         2.10        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
       12.30         9.67         3.39         5.19         6.44         6.74 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8MW TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E7 
       45.67        18.21        37.91        48.79        13.25        34.45 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 
       17.85        13.35        27.35        18.74        52.24         9.04 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA6K 
        4.54        21.04        42.54        12.43 

$`11P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
       32.45         7.69         6.21        33.27        20.09        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       12.16       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        42.77        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       24.03         6.28        30.25         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG 
        8.71        25.12         7.40         3.95         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       12.92        13.48         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S 
       13.41        83.24        52.57        46.09         5.92        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
       15.35         0.10         0.10        12.46        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
       10.52        12.00        12.23        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        7.82         8.02         7.59        14.70         7.04        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30        15.78         7.00        20.02        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
        3.42        15.35         4.44        19.96        22.82         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       15.06        11.24         9.17        15.91        10.16         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         9.44         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12         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-7851 
       23.93        15.42        28.01        18.15        15.32        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-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-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
       12.95        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-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-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-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-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-A487 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         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-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       54.08         4.01        14.01        19.07        12.03         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-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        79.07        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
        7.99        12.36        19.13        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        17.19        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-D7-8579 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-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        14.47        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        17.06        59.54         5.03         0.56         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
        0.23        18.08         1.51         5.92        14.27        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-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-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        0.26        12.95        19.36         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       21.21         3.45        18.81        18.38         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        1.41        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-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73         9.86         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-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-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-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-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       22.19         2.50        12.79         2.70         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-A91Q TCGA-VQ-A91S 
       36.69        11.70        11.93        61.22        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 
             72.23             122.30 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             12.38              13.02 
[1] "0.1 - 72.2 (12.4)"  "0.0 - 122.3 (13.0)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         2        4        8        7        11        12
  11P LOSS WILD-TYPE       9       15       40       25        66        72
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED          12         21          6          9       10
  11P LOSS WILD-TYPE        17         76         66         39       41
                    vv
clus                 STAGE IVA
  11P LOSS MUTATED           1
  11P LOSS WILD-TYPE         3
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  9
  STAGE IA                  4                 15
  STAGE IB                  8                 40
  STAGE II                  7                 25
  STAGE IIA                11                 66
  STAGE IIB                12                 72
  STAGE III                12                 17
  STAGE IIIA               21                 76
  STAGE IIIB                6                 66
  STAGE IIIC                9                 39
  STAGE IV                 10                 41
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11P LOSS MUTATED      10  27  52  16
  11P LOSS WILD-TYPE    43  99 228 108
D62V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               10                 43
  T2                  27                 99
  T3                  52                228
  T4                  16                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
  11P LOSS MUTATED    34  39  15  16
  11P LOSS WILD-TYPE 166 143  81  81
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               34                166
  N1               39                143
  N2               15                 81
  N3               16                 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"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    88   8
  11P LOSS WILD-TYPE 425  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     88    8
  11P LOSS WILD-TYPE  425   31
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               88                425
  1                8                 31
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    25  88
  11P LOSS WILD-TYPE 157 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     25   88
  11P LOSS WILD-TYPE  157  339
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               25                157
  MALE                 88                339
[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                                                       17
  11P LOSS WILD-TYPE                                                    145
                    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                                                 17
  11P LOSS WILD-TYPE                                               61
                    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)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                17
  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)                           145
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  61
  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     0 113
  11P LOSS WILD-TYPE   6 490
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0  113
  11P LOSS WILD-TYPE    6  490
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 0                  6
  YES              113                490
[1] 2 2
[1] FALSE
D62V10, continuous
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    46   3   5   4
  11P LOSS WILD-TYPE 301  15  14  21
D62V11, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               46                301
  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"
D62V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED      28                         2
  11P LOSS WILD-TYPE   101                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           0    68
  11P LOSS WILD-TYPE                                         1   317
D62V13, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                                   28                101
  BLACK OR AFRICAN AMERICAN                                2                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   68                317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  68
  11P LOSS WILD-TYPE   5 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   68
  11P LOSS WILD-TYPE    5  326
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               68                326
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    65  48
  11Q LOSS WILD-TYPE 289 173
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               113                462 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                48                173 
$`11Q LOSS MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A6QS 
        5.92         4.21        20.12        18.64        23.41         9.96 
TCGA-IG-A97I TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OG TCGA-L5-A4OM 
       12.16        42.77         3.16         0.30         4.70        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A893 
        3.32         7.17         3.16         6.94         2.60         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NT TCGA-L7-A6VZ 
       55.50         2.66        13.55        13.22        27.12        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W 
       10.45        12.66        12.43         0.10         0.10        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U6 
       12.59        12.49        12.76         0.10        15.52        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 
       25.25        12.03         0.13         5.06         6.35         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ER 
        1.45        12.69        20.02         3.42        18.81        12.43 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE 
       18.31        28.11        18.18         9.17        15.91         2.10 
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-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
        8.94        16.24        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT 
       20.09         0.85        20.78         2.63         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03         0.79        12.82        14.86         4.67 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       24.03         6.28        30.25         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
        3.68        32.61        19.99        21.01        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
       58.59         4.90        29.00         7.13         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH 
       25.12         0.36         7.40         3.95        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49O 
       13.41        83.24        52.57        46.09         5.92        13.41 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.15        15.35         0.10        12.46        12.59        22.39 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW 
       11.54        12.33        13.22         4.47        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.23        13.18        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04        29.59        53.95         9.30 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       15.78         7.00        20.38         5.29         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW 
        9.27         4.44        19.96        22.82         1.55         8.12 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-X8-AAAR 
       30.71        42.87        46.19        15.06        11.24        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.01         9.47         9.44         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         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-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         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-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-8081 TCGA-BR-8284 
       14.43        11.44         0.69        12.26        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-8366 
        6.18        19.50        13.08         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        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-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-A4J9 
       14.17         0.53        12.82         0.66        19.36         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42        13.64        11.57         5.13         2.83 
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-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-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        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-5725 
        1.02         0.99         6.02         0.99       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-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        7.99        12.36        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       17.85        13.35        17.19        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-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-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        19.53        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 
       59.54         5.03         0.56         5.52        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-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-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-A4H2 TCGA-HU-A4H3 
        6.51         6.25        10.19         0.26        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO 
       18.81         3.39        18.38         5.36        13.08         1.41 
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-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73         9.86         8.52        61.25         6.08 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60        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-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-A923 TCGA-VQ-A924 
       36.16         7.36         9.50         9.73         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-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-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        21.11        10.62         0.79 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.07               0.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              55.5              122.3 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            12.330             12.985 
[1] "0.1 - 55.5 (12.3)"  "0.0 - 122.3 (13.0)"
[1] "hr=" "1.4"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         2        6        3        9        12        12
  11Q LOSS WILD-TYPE       9       13       45       23        65        72
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED          11         18         10         12        9
  11Q LOSS WILD-TYPE        18         79         62         36       42
                    vv
clus                 STAGE IVA
  11Q LOSS MUTATED           2
  11Q LOSS WILD-TYPE         2
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   2                  9
  STAGE IA                  6                 13
  STAGE IB                  3                 45
  STAGE II                  9                 23
  STAGE IIA                12                 65
  STAGE IIB                12                 72
  STAGE III                11                 18
  STAGE IIIA               18                 79
  STAGE IIIB               10                 62
  STAGE IIIC               12                 36
  STAGE IV                  9                 42
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11Q LOSS MUTATED      12  26  52  17
  11Q LOSS WILD-TYPE    41 100 228 107
D63V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               12                 41
  T2                  26                100
  T3                  52                228
  T4                  17                107
[1] 4 2
[1] 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    31  40  14  21
  11Q LOSS WILD-TYPE 169 142  82  76
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               31                169
  N1               40                142
  N2               14                 82
  N3               21                 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"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    87   8
  11Q LOSS WILD-TYPE 426  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     87    8
  11Q LOSS WILD-TYPE  426   31
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               87                426
  1                8                 31
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    23  91
  11Q LOSS WILD-TYPE 159 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     23   91
  11Q LOSS WILD-TYPE  159  336
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               23                159
  MALE                 91                336
[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     0 114
  11Q LOSS WILD-TYPE   6 489
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0  114
  11Q LOSS WILD-TYPE    6  489
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 0                  6
  YES              114                489
[1] 2 2
[1] FALSE
D63V10, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    43   4   2   4
  11Q LOSS WILD-TYPE 304  14  17  21
D63V11, 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"
D63V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED      28                         2
  11Q LOSS WILD-TYPE   101                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           0    71
  11Q LOSS WILD-TYPE                                         1   314
D63V13, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                                   28                101
  BLACK OR AFRICAN AMERICAN                                2                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   71                314
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2  69
  11Q LOSS WILD-TYPE   5 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   69
  11Q LOSS WILD-TYPE    5  325
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               69                325
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    47  40
  12P LOSS WILD-TYPE 307 181
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                87                488 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                40                181 
$`12P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4QS 
       25.78        31.27        13.94        32.45        33.27         3.88 
TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43E 
        0.79        14.50        42.77        25.41        25.22        30.25 
TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A891 
        8.94        32.61         7.17        58.59         7.13         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A7HY 
        3.02        55.50        12.92        52.57        12.66        12.03 
TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-S8-A6BV TCGA-V5-A7RC TCGA-X8-AAAR TCGA-Z6-A8JE 
        7.82         5.06        20.02         3.42        10.16         2.10 
TCGA-ZR-A9CJ TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 
       19.73         6.61         6.18        17.29        35.24        15.42 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8687 
        3.45        11.44         5.39         9.21         9.86         8.22 
TCGA-BR-A4J6 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8535 TCGA-CD-A486 
        0.66        13.15         0.30         0.07         0.13         3.42 
TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4477 
       11.31        12.20        20.02         7.99        29.98        30.97 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-5647 
       15.02        69.04        15.22        12.33        14.27         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4H2 
        7.99        72.23         0.56        12.59        11.77        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-R5-A7O7 TCGA-VQ-A8DU 
       23.84        12.30         5.19        13.08        45.67         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY 
       13.02        12.79         2.70        13.35        27.35        14.33 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94T 
        9.50        52.24         2.01         4.54        21.04        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       40.08        16.14         0.79 

$`12P LOSS WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21         7.69         6.21        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI 
        0.30         4.31        24.00         3.68         4.70        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI 
       25.12         0.36         7.40         2.66        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        83.24        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35         0.10        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.00        12.23        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        5.16         8.02         7.59        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         5.29         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         4.44        18.81        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        3.42         2.66        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         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-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        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-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-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-8686 
        7.53         0.49        11.54        15.81        16.44        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-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17         0.53        12.82        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-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        2.83         3.25        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-8533 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-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-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        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-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        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-D7-6520 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-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        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-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-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-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-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-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        14.27        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-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        2.10        19.36         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-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-A7ZE 
       20.15        37.64         3.72        19.73         9.86        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-A8DV 
       16.87        19.04         5.79         0.92        48.79        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-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-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       26.24        64.57        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-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        7.36         9.73         9.04        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 
       64.18         2.66        42.54        22.09        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       32.94        29.98        17.13        54.12        26.04        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       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 
             12.59              12.79 
[1] "0.1 - 72.2 (12.6)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         3        4        9        4        11        12
  12P LOSS WILD-TYPE       8       15       39       28        66        72
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           2         16         10          8        6
  12P LOSS WILD-TYPE        27         81         62         40       45
                    vv
clus                 STAGE IVA
  12P LOSS MUTATED           0
  12P LOSS WILD-TYPE         4
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  4                 15
  STAGE IB                  9                 39
  STAGE II                  4                 28
  STAGE IIA                11                 66
  STAGE IIB                12                 72
  STAGE III                 2                 27
  STAGE IIIA               16                 81
  STAGE IIIB               10                 62
  STAGE IIIC                8                 40
  STAGE IV                  6                 45
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12P LOSS MUTATED      11  20  46  11
  12P LOSS WILD-TYPE    42 106 234 113
D64V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1               11                 42
  T2                  20                106
  T3                  46                234
  T4                  11                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
  12P LOSS MUTATED    31  26  16  14
  12P LOSS WILD-TYPE 169 156  80  83
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               31                169
  N1               26                156
  N2               16                 80
  N3               14                 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"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    76   5
  12P LOSS WILD-TYPE 437  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     76    5
  12P LOSS WILD-TYPE  437   34
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               76                437
  1                5                 34
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    31  61
  12P LOSS WILD-TYPE 151 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     31   61
  12P LOSS WILD-TYPE  151  366
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               31                151
  MALE                 61                366
[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  91
  12P LOSS WILD-TYPE   5 512
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   91
  12P LOSS WILD-TYPE    5  512
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 1                  5
  YES               91                512
[1] 2 2
[1] FALSE
D64V10, continuous
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    44   2   4   5
  12P LOSS WILD-TYPE 303  16  15  20
D64V11, 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"
D64V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED      16                         4
  12P LOSS WILD-TYPE   113                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           0    56
  12P LOSS WILD-TYPE                                         1   329
D64V13, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                                   16                113
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   56                329
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  50
  12P LOSS WILD-TYPE   6 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   50
  12P LOSS WILD-TYPE    6  344
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               50                344
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    38  36
  12Q LOSS WILD-TYPE 316 185
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                74                501 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                36                185 
$`12Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 
       31.27        13.94        33.27         3.88         0.79        23.41 
TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43M 
       14.50        42.77        25.41        25.22        30.25         8.94 
TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A893 TCGA-L5-A8NE 
       32.61         7.17        58.59         7.13         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-S8-A6BV 
        2.66        12.92         7.82         5.06         2.89        20.02 
TCGA-V5-A7RC TCGA-V5-AASX TCGA-VR-A8ET TCGA-X8-AAAR TCGA-BR-4183 TCGA-BR-6456 
        3.42         4.44         1.55        10.16         6.61        17.29 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8483 
       35.24        15.42         3.45        11.44        12.95         5.39 
TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4J6 TCGA-CD-5802 TCGA-CD-A489 
        9.21         9.86         8.22         0.66         0.30        11.31 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-5725 TCGA-CG-5732 
       12.20        20.02         7.99        29.98        15.02        69.04 
TCGA-D7-6528 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-8211 TCGA-FP-8631 
       15.22        15.65         0.62         7.99        13.58         0.56 
TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-IN-A6RP TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
       11.77        12.95         6.44        37.64        45.67        18.21 
TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU 
        5.46        18.48        12.79        17.85        13.35        27.35 
TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6I 
       52.24         4.54        21.04        11.24        40.08        16.14 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`12Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69         6.21        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       12.16       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         0.30         4.31        24.00         3.68         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       19.99        21.01        47.93        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        3.16         4.90        29.00         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG 
        2.60        25.12         0.36         7.40         3.95        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN 
       12.03        13.18         0.13        33.11         5.16         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         1.45        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        5.29         4.80        15.35         9.27        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        42.87        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       15.91         3.42         2.10         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       11.70        19.56        11.01         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-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-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-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-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72        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-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-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        12.82 
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-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18         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-A48A TCGA-CD-A48C 
        0.13         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-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 
            12.855             12.760 
[1] "0.3 - 69.0 (12.9)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         3        3        6        3         8        14
  12Q LOSS WILD-TYPE       8       16       42       29        69        70
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0         12          9          8        4
  12Q LOSS WILD-TYPE        29         85         63         40       47
                    vv
clus                 STAGE IVA
  12Q LOSS MUTATED           1
  12Q LOSS WILD-TYPE         3
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  3                 16
  STAGE IB                  6                 42
  STAGE II                  3                 29
  STAGE IIA                 8                 69
  STAGE IIB                14                 70
  STAGE III                 0                 29
  STAGE IIIA               12                 85
  STAGE IIIB                9                 63
  STAGE IIIC                8                 40
  STAGE IV                  4                 47
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12Q LOSS MUTATED      12  12  39  10
  12Q LOSS WILD-TYPE    41 114 241 114
D65V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               12                 41
  T2                  12                114
  T3                  39                241
  T4                  10                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
  12Q LOSS MUTATED    26  19  14  13
  12Q LOSS WILD-TYPE 174 163  82  84
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               26                174
  N1               19                163
  N2               14                 82
  N3               13                 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"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    62   4
  12Q LOSS WILD-TYPE 451  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     62    4
  12Q LOSS WILD-TYPE  451   35
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               62                451
  1                4                 35
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    27  52
  12Q LOSS WILD-TYPE 155 375
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     27   52
  12Q LOSS WILD-TYPE  155  375
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               27                155
  MALE                 52                375
[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                                                       20
  12Q LOSS WILD-TYPE                                                    142
                    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)                          20
  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)                           142
  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  78
  12Q LOSS WILD-TYPE   5 525
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   78
  12Q LOSS WILD-TYPE    5  525
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 1                  5
  YES               78                525
[1] 2 2
[1] FALSE
D65V10, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    36   4   2   3
  12Q LOSS WILD-TYPE 311  14  17  22
D65V11, 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"
D65V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED       8                         3
  12Q LOSS WILD-TYPE   121                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0    56
  12Q LOSS WILD-TYPE                                         1   329
D65V13, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                                    8                121
  BLACK OR AFRICAN AMERICAN                                3                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   56                329
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  41
  12Q LOSS WILD-TYPE   6 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   41
  12Q LOSS WILD-TYPE    6  353
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               41                353
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    54  38
  13Q LOSS WILD-TYPE 300 183
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                92                483 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                38                183 
$`13Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE 
       25.78        58.55         7.63         8.94        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
       20.09         0.85        20.78         3.88         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A93E 
       23.41         9.96        44.75        60.39        68.02        25.22 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
       24.00         3.68        21.01        47.93         3.16        29.00 
TCGA-L5-A891 TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
        3.95        13.22         5.49        13.41        83.24        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       15.35        13.25        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
        0.10        13.22        12.33        10.52        12.23        12.03 
TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-VR-A8EO TCGA-VR-A8EP 
        0.13         5.06         6.35        12.69        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I 
       22.82        18.31        28.11        18.18        42.87        15.91 
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-8525 
        7.40        19.50        20.22         9.86        12.89         0.07 
TCGA-CD-8526 TCGA-CD-8533 TCGA-CG-4301 TCGA-CG-4466 TCGA-CG-4475 TCGA-D7-6525 
        0.07         0.13         3.02        18.97        22.98        13.35 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-FP-7916 TCGA-FP-8211 TCGA-HU-A4GC 
       18.21        21.14        16.44        14.07        13.58         3.25 
TCGA-HU-A4H2 TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-RD-A7BS TCGA-VQ-A8P5 TCGA-VQ-A8PM 
       12.95         5.36         6.74        11.05         7.73         1.87 
TCGA-VQ-A91Z TCGA-VQ-A925 
       52.24         4.54 

$`13Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        6.21        33.27         2.63        20.12        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
        0.79        12.82        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
      122.10         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        0.30         4.31         8.94         4.70        32.61        19.99 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49V 
        8.71        27.12        52.57        46.09        12.66         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10        12.46        12.59        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
        4.47        25.25        12.00        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59        14.70         7.04        29.59 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       20.02        20.38         5.29         3.42         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY 
        9.27         4.44        12.43         1.55         8.12        30.71 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD 
       46.19        15.06        11.24         9.17        10.16         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.01         9.47         9.44         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-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-6565 TCGA-BR-6566 
       13.87        13.68        19.33        39.12         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-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-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-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        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-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-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 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-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-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-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-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        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-D7-8576 TCGA-D7-8579 
       24.72        16.80        19.50        17.19        14.66        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        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-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       19.53        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BF TCGA-FP-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-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-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-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
        5.19        13.08         1.41         6.44        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-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-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        35.24        21.73 
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-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-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-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-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-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-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 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.00 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             83.24             122.30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             13.05              12.66 
[1] "0.1 - 83.2 (13.1)"  "0.0 - 122.3 (12.7)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         3        3        4        2        16        16
  13Q LOSS WILD-TYPE       8       16       44       30        61        68
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED          12         17          9          5        4
  13Q LOSS WILD-TYPE        17         80         63         43       47
                    vv
clus                 STAGE IVA
  13Q LOSS MUTATED           1
  13Q LOSS WILD-TYPE         3
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  3                 16
  STAGE IB                  4                 44
  STAGE II                  2                 30
  STAGE IIA                16                 61
  STAGE IIB                16                 68
  STAGE III                12                 17
  STAGE IIIA               17                 80
  STAGE IIIB                9                 63
  STAGE IIIC                5                 43
  STAGE IV                  4                 47
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  13Q LOSS MUTATED      12  19  52  11
  13Q LOSS WILD-TYPE    41 107 228 113
D66V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               12                 41
  T2                  19                107
  T3                  52                228
  T4                  11                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
  13Q LOSS MUTATED    36  38  10   9
  13Q LOSS WILD-TYPE 164 144  86  88
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               36                164
  N1               38                144
  N2               10                 86
  N3                9                 88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    82   3
  13Q LOSS WILD-TYPE 431  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     82    3
  13Q LOSS WILD-TYPE  431   36
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               82                431
  1                3                 36
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    20  77
  13Q LOSS WILD-TYPE 162 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     20   77
  13Q LOSS WILD-TYPE  162  350
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               20                162
  MALE                 77                350
[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                                                          2
  13Q LOSS WILD-TYPE                                                       19
                    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                         2
  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                          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"
D66V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     2  95
  13Q LOSS WILD-TYPE   4 508
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   95
  13Q LOSS WILD-TYPE    4  508
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 2                  4
  YES               95                508
[1] 2 2
[1] FALSE
D66V10, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    26   3   2   4
  13Q LOSS WILD-TYPE 321  15  17  21
D66V11, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               26                321
  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"
D66V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED      31                         0
  13Q LOSS WILD-TYPE    98                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           0    55
  13Q LOSS WILD-TYPE                                         1   330
D66V13, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                                   31                 98
  BLACK OR AFRICAN AMERICAN                                0                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   55                330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  58
  13Q LOSS WILD-TYPE   6 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   58
  13Q LOSS WILD-TYPE    6  336
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               58                336
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    91  57
  14Q LOSS WILD-TYPE 263 164
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               148                427 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                57                164 
$`14Q LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
        7.63         8.94        16.24         4.21        32.45        20.09 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB 
       23.41        12.82         4.67        14.50       122.10        60.39 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        25.22         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y 
        4.70        32.61         3.16         7.13         6.94         0.36 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L 
        3.95        55.50         2.66        16.47        10.36        10.45 
TCGA-LN-A49W TCGA-LN-A7HV TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ 
       13.25        10.52        33.11         7.59         5.06         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8Q7 
        9.30        15.78         7.00        18.81        22.82        42.87 
TCGA-VR-AA4G TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       15.06         2.10         2.66        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4279 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 
        6.61         9.57        19.33        26.10         9.17        12.16 
TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 
       31.20        35.24        15.42        28.01        28.73        18.71 
TCGA-BR-8058 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 
       17.49        12.95         2.66        14.79         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A4CS TCGA-BR-A4J1 
       25.18         9.21        11.54        15.68         1.48         0.72 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 
        0.66        19.36         0.46        20.65         1.15        13.18 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 
        0.07         0.07         0.07         0.13         0.13        11.31 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4477 
       12.20        20.02         7.99         8.05        54.08        30.97 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       20.55        18.84        18.54        17.19        10.26        15.98 
TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 
       14.66        16.44        11.31         2.96         7.40         7.99 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8245 
       11.38        14.07        17.06         0.56        26.47        12.59 
TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H4 
       14.17         3.25        11.77         8.98         2.10        23.84 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU 
       27.42        21.21         5.19         6.44         6.74         1.81 
TCGA-IP-7968 TCGA-KB-A93H TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
        2.53        37.64        16.67        37.91       115.69         8.94 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        5.46        13.02        18.48        35.24         7.73        46.26 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       12.79         2.70        17.85        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94U 
       65.16        20.81        52.24        64.18        21.04        22.09 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       32.94        29.98        26.04         0.79 

$`14Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        0.79         9.96        14.86        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI 
       24.03         6.28         3.16        30.25         4.31        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
       58.59         4.90        29.00         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         7.40         3.02        35.97        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        46.09         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        13.18         0.13         5.16         7.82         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC 
       14.70         7.04        29.59        53.95         2.89         1.45 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
       15.35         9.27         4.44        19.96        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       18.31         8.12        28.11        30.71        18.18        46.19 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       11.24         9.17        15.91        10.16         3.42        19.73 
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 
             122.1              122.3 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            12.985             12.660 
[1] "0.1 - 122.1 (13.0)" "0.0 - 122.3 (12.7)"
[1] "hr=" "1"  
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         4        3        9       11        18        21
  14Q LOSS WILD-TYPE       7       16       39       21        59        63
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           7         31         21         11        5
  14Q LOSS WILD-TYPE        22         66         51         37       46
                    vv
clus                 STAGE IVA
  14Q LOSS MUTATED           3
  14Q LOSS WILD-TYPE         1
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   4                  7
  STAGE IA                  3                 16
  STAGE IB                  9                 39
  STAGE II                 11                 21
  STAGE IIA                18                 59
  STAGE IIB                21                 63
  STAGE III                 7                 22
  STAGE IIIA               31                 66
  STAGE IIIB               21                 51
  STAGE IIIC               11                 37
  STAGE IV                  5                 46
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  14Q LOSS MUTATED      12  26  82  27
  14Q LOSS WILD-TYPE    41 100 198  97
D67V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1               12                 41
  T2                  26                100
  T3                  82                198
  T4                  27                 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
  14Q LOSS MUTATED    47  45  32  20
  14Q LOSS WILD-TYPE 153 137  64  77
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               47                153
  N1               45                137
  N2               32                 64
  N3               20                 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"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   130   6
  14Q LOSS WILD-TYPE 383  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    130    6
  14Q LOSS WILD-TYPE  383   33
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              130                383
  1                6                 33
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    45 110
  14Q LOSS WILD-TYPE 137 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     45  110
  14Q LOSS WILD-TYPE  137  317
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               45                137
  MALE                110                317
[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     1 154
  14Q LOSS WILD-TYPE   5 449
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1  154
  14Q LOSS WILD-TYPE    5  449
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 1                  5
  YES              154                449
[1] 2 2
[1] FALSE
D67V10, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    90   3   2   7
  14Q LOSS WILD-TYPE 257  15  17  18
D67V11, 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"
D67V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED      30                         3
  14Q LOSS WILD-TYPE    99                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           0   105
  14Q LOSS WILD-TYPE                                         1   280
D67V13, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                                   30                 99
  BLACK OR AFRICAN AMERICAN                                3                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  105                280
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  97
  14Q LOSS WILD-TYPE   6 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   97
  14Q LOSS WILD-TYPE    6  297
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               97                297
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    87  47
  15Q LOSS WILD-TYPE 267 174
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               134                441 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                47                174 
$`15Q LOSS MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YC 
        5.92        16.24        32.45         7.69        20.09        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A938 TCGA-JY-A93C 
       18.64         3.88         4.67        14.50        25.41        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       31.56        25.22         0.30         8.94        24.00         4.70 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NE 
       32.61        47.93         4.90        29.00         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NR 
        2.66        35.97        12.92        13.48         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MQ 
       13.41        27.12        83.24        12.59        22.39        12.33 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-RE-A7BO 
       12.33        25.25        12.03         5.06        29.59         7.00 
TCGA-S8-A6BV TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EU TCGA-X8-AAAR TCGA-Z6-A8JE 
       20.02         4.80        18.81        18.31        10.16         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7901 
        2.66        19.73        11.01        35.24        28.73         3.45 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8686 TCGA-BR-8690 
       12.95         2.66        14.79         5.39        15.68        10.68 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8526 
        0.72        20.65        13.64        13.18         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.07         0.16         0.13        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5724 
       20.02         7.99         4.01        18.97         1.02        12.03 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       12.66        19.13        20.55        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       12.79        14.66        16.44        11.31         2.96        15.65 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-7998 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 
        7.40         7.99        22.29         5.52         0.23        26.47 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU 
       12.59        14.17        12.10        22.75         8.98         6.25 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RJ 
        2.10        12.95        23.84         9.67        27.42         5.36 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IP-7968 TCGA-MX-A663 TCGA-R5-A7ZF 
        5.19         6.44         1.81         2.53         9.86         8.52 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB 
       11.05        16.67        37.91       115.69        35.61         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91U 
       48.79         5.46        13.35        27.35        65.16         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA68 
        9.50         9.73         9.04        42.54        22.09        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6F 
       29.98        54.12 

$`15Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94         4.21         6.21        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82         9.96        14.86        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       60.39        68.02         3.68        41.52        42.77        21.70 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         4.31         3.68 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        3.16        58.59         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ 
        2.60        25.12         0.36         7.40         3.95        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW 
       13.55        13.22         7.76        21.37        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.49        12.76        12.59         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       11.54        13.22         4.47        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         1.45        12.69        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        3.42        15.35         9.27         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
        3.42        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-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-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        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-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-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-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        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-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        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-A4J8 TCGA-BR-A4J9 
        0.53        12.82         0.66        19.36        13.51         0.46 
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-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8529 
       13.15         0.30         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-AA64 
        5.72        64.18        21.04         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        32.94        17.13        26.04        16.14        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       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 
            12.625             12.790 
[1] "0.1 - 115.7 (12.6)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         3        1       10        7        16        20
  15Q LOSS WILD-TYPE       8       18       38       25        61        64
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           8         30         18         10       10
  15Q LOSS WILD-TYPE        21         67         54         38       41
                    vv
clus                 STAGE IVA
  15Q LOSS MUTATED           2
  15Q LOSS WILD-TYPE         2
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  1                 18
  STAGE IB                 10                 38
  STAGE II                  7                 25
  STAGE IIA                16                 61
  STAGE IIB                20                 64
  STAGE III                 8                 21
  STAGE IIIA               30                 67
  STAGE IIIB               18                 54
  STAGE IIIC               10                 38
  STAGE IV                 10                 41
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  15Q LOSS MUTATED      13  26  81  18
  15Q LOSS WILD-TYPE    40 100 199 106
D68V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1               13                 40
  T2                  26                100
  T3                  81                199
  T4                  18                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
  15Q LOSS MUTATED    42  48  24  21
  15Q LOSS WILD-TYPE 158 134  72  76
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               42                158
  N1               48                134
  N2               24                 72
  N3               21                 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"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   118  10
  15Q LOSS WILD-TYPE 395  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    118   10
  15Q LOSS WILD-TYPE  395   29
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              118                395
  1               10                 29
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    41 101
  15Q LOSS WILD-TYPE 141 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     41  101
  15Q LOSS WILD-TYPE  141  326
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               41                141
  MALE                101                326
[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                                                          2
  15Q LOSS WILD-TYPE                                                       19
                    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                                          5
  15Q LOSS WILD-TYPE                                        8
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                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         5
                                                                   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                          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"
D68V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3 139
  15Q LOSS WILD-TYPE   3 464
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3  139
  15Q LOSS WILD-TYPE    3  464
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 3                  3
  YES              139                464
[1] 2 2
[1] FALSE
D68V10, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    75   4   3   3
  15Q LOSS WILD-TYPE 272  14  16  22
D68V11, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               75                272
  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"
D68V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED      34                         1
  15Q LOSS WILD-TYPE    95                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           0    92
  15Q LOSS WILD-TYPE                                         1   293
D68V13, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                                   34                 95
  BLACK OR AFRICAN AMERICAN                                1                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   92                293
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  91
  15Q LOSS WILD-TYPE   6 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   91
  15Q LOSS WILD-TYPE    6  303
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               91                303
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    89  56
  16P LOSS WILD-TYPE 265 165
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               145                430 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                56                165 
$`16P LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3YC 
        7.63         5.92        13.94         8.94        32.45        20.12 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OE 
       42.77        25.41        23.18        25.22         3.16        24.00 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        4.70        32.61        21.01         3.16        58.59         4.90 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NN 
        0.36         7.40         3.95         3.02        12.92         5.49 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       83.24        52.57        46.09        10.45        12.43        13.41 
TCGA-LN-A49V TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A7HW TCGA-Q9-A6FU TCGA-R6-A6DN 
        0.10        22.39        12.33        12.00         5.16         8.02 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP 
        7.00         5.29         3.42         4.80         9.27        19.96 
TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-BR-4183 TCGA-BR-7197 
       22.82        42.87         2.10         2.66         6.61         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 
       35.24        15.42        28.01         3.45        18.71        11.44 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 
        0.69        12.95         2.66        16.31        17.52        14.79 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        0.49        11.54         8.22        22.26         1.48         0.72 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        1.15        13.64         0.07         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4436 
        0.16         3.42        12.43        11.61        12.20         7.99 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6519 
       29.98        19.07        12.03        12.03        11.93        20.55 
TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       15.22        12.33        11.31         2.96        15.65         8.38 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-HU-8243 TCGA-HU-8245 
        7.40         7.99        16.24        72.23         5.92        12.59 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU 
       12.10         0.76        22.75        25.81        11.77         6.25 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RN TCGA-IN-A6RR 
       23.84        12.30         9.67        27.42        13.08         6.74 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 
        5.56        37.64         6.08         9.24        11.05        16.67 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PC 
       35.61         5.79        48.79         5.46        18.48        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU 
       22.19        12.79         2.70        17.85         1.87        27.35 
TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       64.57        36.69        18.74         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-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30        58.55        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.50        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
        3.68        41.52        21.70        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI 
       30.25         0.30         4.31         8.94         3.68        19.99 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU 
       47.93        18.35         3.32         7.17         1.38        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        35.97        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76        21.37         8.71        13.41        27.12 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.36         5.92        12.66         0.10        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59         0.10        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.13        33.11         7.82         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV 
        7.04        29.59        15.78        20.02        20.38        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        4.44        18.81        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        30.71        18.18        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-5816 
        9.17        15.91        10.16         3.42        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       11.70        19.56        11.01         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-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-7703 TCGA-BR-7707 TCGA-BR-7717 
       31.20        32.94        12.82        24.76        23.93        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       15.32        28.73        12.43         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        12.26         9.60        20.55         8.05         0.56 
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-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-8680 
       15.81         9.34        13.45         6.28         7.53        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-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-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8528 
        3.25        13.15        13.18         0.30         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-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        9.34        11.31         6.58         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        47.05        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-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-D7-6518 TCGA-D7-6520 
       21.07         7.99        12.36        12.66        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        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-A748 TCGA-D7-A74B 
       13.71        11.24        11.44         9.76         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62        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-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-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.27        14.17        11.41        10.62        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN 
       12.30        11.84        24.20         3.25        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.95        19.36         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-A6RO 
       18.81         3.39        18.38         5.36         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44        12.59         6.51         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-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-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92        13.25        13.02        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-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.50         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       14.33        65.16        11.70        11.93        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 
       22.68         1.71        36.16         7.36         9.73         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-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        11.24        18.41        28.41        29.98        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        12.43        10.62 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             83.24             122.30 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            12.030             13.115 
[1] "0.1 - 83.2 (12.0)"  "0.0 - 122.3 (13.1)"
[1] "hr=" "1"  
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         4        6       11        9        19        19
  16P LOSS WILD-TYPE       7       13       37       23        58        65
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           7         28         17          9        9
  16P LOSS WILD-TYPE        22         69         55         39       42
                    vv
clus                 STAGE IVA
  16P LOSS MUTATED           0
  16P LOSS WILD-TYPE         4
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   4                  7
  STAGE IA                  6                 13
  STAGE IB                 11                 37
  STAGE II                  9                 23
  STAGE IIA                19                 58
  STAGE IIB                19                 65
  STAGE III                 7                 22
  STAGE IIIA               28                 69
  STAGE IIIB               17                 55
  STAGE IIIC                9                 39
  STAGE IV                  9                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16P LOSS MUTATED      17  27  74  24
  16P LOSS WILD-TYPE    36  99 206 100
D69V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1               17                 36
  T2                  27                 99
  T3                  74                206
  T4                  24                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
  16P LOSS MUTATED    48  53  21  19
  16P LOSS WILD-TYPE 152 129  75  78
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               48                152
  N1               53                129
  N2               21                 75
  N3               19                 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"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   132   5
  16P LOSS WILD-TYPE 381  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    132    5
  16P LOSS WILD-TYPE  381   34
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0              132                381
  1                5                 34
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    45 109
  16P LOSS WILD-TYPE 137 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     45  109
  16P LOSS WILD-TYPE  137  318
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               45                137
  MALE                109                318
[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                                                       32
  16P LOSS WILD-TYPE                                                    130
                    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                                                 28
  16P LOSS WILD-TYPE                                               50
                    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)                          32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                28
  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)                           130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  50
  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     2 152
  16P LOSS WILD-TYPE   4 451
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2  152
  16P LOSS WILD-TYPE    4  451
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 2                  4
  YES              152                451
[1] 2 2
[1] FALSE
D69V10, continuous
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    81   5   2   5
  16P LOSS WILD-TYPE 266  13  17  20
D69V11, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               81                266
  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"
D69V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED      33                         5
  16P LOSS WILD-TYPE    96                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           0    95
  16P LOSS WILD-TYPE                                         1   290
D69V13, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                                   33                 96
  BLACK OR AFRICAN AMERICAN                                5                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   95                290
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  90
  16P LOSS WILD-TYPE   4 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   90
  16P LOSS WILD-TYPE    4  304
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               90                304
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    99  57
  16Q LOSS WILD-TYPE 255 164
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               156                419 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                57                164 
$`16Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       31.27         7.63         5.92         8.94        16.24        32.45 
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C 
       20.09        20.12        14.50        42.77        25.41        23.18 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16         8.94        24.00         4.70        32.61        21.01 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        3.16        58.59         4.90         0.36         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
       55.50         5.49         8.71        83.24        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-Q9-A6FU 
       10.45        13.41         0.10        12.33        10.52         5.16 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        5.06         6.35        53.95         9.30         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP 
       12.69         7.00         5.29         4.80         9.27        19.96 
TCGA-VR-A8EQ TCGA-Z6-AAPN TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6564 
       22.82         2.66         9.44         6.61        17.29        26.10 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 
        9.21        35.24        15.42        28.01        28.73         3.45 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 
       18.71        11.44         0.69         9.60        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 
       16.31        17.52        14.79        25.18         0.49        11.54 
TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 
        8.22         0.72        20.65         1.15        13.64        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 
        0.30         0.07         0.07         0.07         0.07         0.16 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4444 
        3.42        12.43        12.20         7.99        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5724 TCGA-D7-5579 
       19.07        12.03        22.98        30.97        12.03        11.93 
TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-A4YT 
       20.55        17.19        15.22        12.79        18.21        14.27 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-EQ-A4SO TCGA-F1-6875 
       11.31         2.96        15.65         8.38        16.24        72.23 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GH TCGA-HU-A4GU 
        5.92        12.59        12.10         0.76        11.77         6.25 
TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI 
        0.26        23.84        12.30         9.67        27.42        18.38 
TCGA-IN-A6RN TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7ZR 
       13.08         5.56        60.56        20.15        37.64         6.08 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
        9.24        11.05        35.61         5.79        48.79         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       18.48         7.73        46.26        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91N 
       17.85         1.87        27.35        64.57        36.69        18.74 
TCGA-VQ-A91S TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       22.68         9.50         9.73        52.24         9.04         4.54 
TCGA-VQ-A92D TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-ZQ-A9CR 
       64.18        22.09        40.08        32.94        17.13         0.79 

$`16Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       25.78        14.30        58.55        13.94         4.21         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 
        6.21        33.27         0.85        20.78         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       44.75        60.39        68.02         3.68        41.52        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        4.31         3.68        19.99        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         1.38        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG 
        8.71         2.60        25.12         7.40         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M 
       21.37        13.41        27.12        52.57         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       12.43         0.10        13.15        15.35        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        11.54        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        12.00        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       29.59        15.78        20.02        20.38         3.42        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        4.44        18.81        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        10.16         3.42         2.10 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
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-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
       12.43         9.07        12.76        17.49        14.43        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       20.55         8.05         0.56         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        6.18        19.50        13.08         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
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-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
        7.53        15.81        16.44         9.86        15.68        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-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       12.82         0.66        19.36        13.51         0.46        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8527 
       11.57         5.13         2.83         3.25        13.18         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-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         9.34        11.31        11.61         6.58         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-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4460 TCGA-CG-4462 
        8.05        54.08         4.01        14.01        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        12.00         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       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-D7-6518 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-D7-6527 TCGA-D7-6815 TCGA-D7-6818 
       18.61        17.85        13.35        10.26        15.98        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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        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-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34         7.40         7.13         0.62         7.99        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
        0.23        18.08        26.47         1.51        14.27        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       11.41        10.62        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.51        10.19         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       19.36         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39         5.36         5.19         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-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        2.53         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        8.52        61.25         4.60         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-VQ-A8DL TCGA-VQ-A8DV 
       57.44         8.94        16.87        19.04         0.92        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-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       28.96        34.29        16.31         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        13.35        26.24        14.33        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        20.81         1.71        36.16         7.36 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        11.24        18.41        28.41        29.98        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 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             83.24             122.30 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            12.315             12.820 
[1] "0.1 - 83.2 (12.3)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         5        6       12       12        17        20
  16Q LOSS WILD-TYPE       6       13       36       20        60        64
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           8         31         18         11        8
  16Q LOSS WILD-TYPE        21         66         54         37       43
                    vv
clus                 STAGE IVA
  16Q LOSS MUTATED           1
  16Q LOSS WILD-TYPE         3
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   5                  6
  STAGE IA                  6                 13
  STAGE IB                 12                 36
  STAGE II                 12                 20
  STAGE IIA                17                 60
  STAGE IIB                20                 64
  STAGE III                 8                 21
  STAGE IIIA               31                 66
  STAGE IIIB               18                 54
  STAGE IIIC               11                 37
  STAGE IV                  8                 43
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16Q LOSS MUTATED      17  28  81  28
  16Q LOSS WILD-TYPE    36  98 199  96
D70V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               17                 36
  T2                  28                 98
  T3                  81                199
  T4                  28                 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
  16Q LOSS MUTATED    51  50  25  24
  16Q LOSS WILD-TYPE 149 132  71  73
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               51                149
  N1               50                132
  N2               25                 71
  N3               24                 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"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   142   5
  16Q LOSS WILD-TYPE 371  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    142    5
  16Q LOSS WILD-TYPE  371   34
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              142                371
  1                5                 34
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    52 112
  16Q LOSS WILD-TYPE 130 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     52  112
  16Q LOSS WILD-TYPE  130  315
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               52                130
  MALE                112                315
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16Q LOSS MUTATED                                      12
  16Q LOSS WILD-TYPE                                    59
                    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                                                 31
  16Q LOSS WILD-TYPE                                               47
                    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                                           12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                31
  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                                             59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  47
  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     3 161
  16Q LOSS WILD-TYPE   3 442
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3  161
  16Q LOSS WILD-TYPE    3  442
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 3                  3
  YES              161                442
[1] 2 2
[1] FALSE
D70V10, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    93   5   4   4
  16Q LOSS WILD-TYPE 254  13  15  21
D70V11, 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"
D70V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED      32                         4
  16Q LOSS WILD-TYPE    97                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           0   100
  16Q LOSS WILD-TYPE                                         1   285
D70V13, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                                   32                 97
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  100                285
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3  93
  16Q LOSS WILD-TYPE   4 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   93
  16Q LOSS WILD-TYPE    4  301
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               93                301
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   135  87
  17P LOSS WILD-TYPE 219 134
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               222                353 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                87                134 
$`17P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       25.78         7.63         5.92         8.94         4.21        32.45 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6F8 
       18.64         3.88         0.79        23.41        14.50       122.10 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        25.41        31.56        30.25        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OW 
        4.70        32.61         3.32         7.17         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NL 
        7.43         2.60         0.36         3.95        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49K 
        5.49         8.71        13.41        27.12        83.24         5.92 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A7HV TCGA-LN-A7HZ 
       10.45        13.15        13.25        12.59        10.52        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         5.16         7.82         7.59         7.04        29.59 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         1.45        12.69         7.00        20.02 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR 
       12.43         8.12        18.18        42.87        11.24        10.16 
TCGA-Z6-AAPN TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4267 
        2.66        11.70        11.01         9.44         6.61         6.18 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7704 
       17.29        19.33         9.17        12.16         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 
       15.42        28.73        18.71         0.69         9.60        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8373 
        2.66        16.31        15.58        13.08        14.04        14.79 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 
        5.39        25.18        11.54        16.44         9.86        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 
       13.87         7.53        22.26         1.48         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 
       20.65        20.42         1.15         3.25        13.15         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.07         0.10         0.13         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
        3.42        11.31        12.43        11.61        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         7.99         8.05        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 
       29.98        47.05        19.07         7.07        30.97         1.02 
TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 
       15.02        79.07         4.01        69.04        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.54        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 
       15.98        11.31        14.66        16.44        11.31        15.65 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 
        7.40         7.99        11.38        14.07        17.06        13.58 
TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD 
        0.23         1.51        12.59        14.17        12.10        22.75 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 
       11.77         8.98         6.25         2.10        12.95        12.30 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO 
       21.21        18.81         3.39        18.38         5.19         1.41 
TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H 
       12.59         1.81         7.82         2.53         5.56        37.64 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 
        9.86        45.67         9.24         8.61        16.67       115.69 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       18.48        35.24         7.73        46.26        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       17.85         1.87        13.35        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A92D 
       65.16        18.74        20.81        36.16         9.50        64.18 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        22.09        18.41        40.08        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       54.12        26.04        16.14        21.11        12.43         0.79 

$`17P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE 
       31.27        14.30        58.55        13.94        16.24         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.12         9.30         0.53        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         4.67        12.16        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F 
        3.68        41.52        21.70        23.18        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
        6.28         3.16         0.30         4.31         8.94        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        47.93        18.35         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
       29.00         6.94         8.71        25.12         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
       55.50         2.66        35.97        12.92        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M 
        7.76        21.37        52.57        46.09        10.36        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.43        13.41         0.10        15.35         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-R6-A6DN 
       25.25        12.00        12.23        12.03         0.13         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-S8-A6BW 
        5.06        14.70         6.35        53.95         2.89        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
        5.29         3.42        18.81         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       30.71        46.19        15.06         9.17        15.91         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 
        2.10        19.73        26.70        19.56         9.47         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        18.35        30.90         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-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         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-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-8081 
       12.76        17.49        14.43        11.44        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        8.05         0.56         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-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-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-8686 
       13.45         6.28         7.53         0.49        15.81        15.68 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        8.22        12.56         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-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
        0.46        13.64        11.57         5.13         2.83        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.30         0.07         0.07         0.16         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 
        0.10         9.34         6.58         0.10        12.62        15.95 
TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        1.02        14.01        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       18.97        12.00        22.98         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6522 
       21.07         7.99        12.36        12.66        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       17.85        12.79        10.55        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-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-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF 
       19.53        22.29        59.54         5.03         0.56         5.52 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 
       18.08        26.47         5.92        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-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
        3.25        25.81        21.37        29.98         0.10         6.51 
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-7808 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
        8.81        27.42         3.45         5.36        13.08         6.44 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G 
        6.74         6.51         5.56        13.51        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73        18.21         8.52        61.25         6.08 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        4.60        11.05         5.13       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       48.79        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       34.29        16.31        22.19         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       15.65        26.24        36.69        11.70        11.93        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       22.68         1.71         7.36         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-AA69 TCGA-VQ-AA6A TCGA-ZA-A8F6 
        2.66        42.54        28.41        32.94        10.62 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.07               0.00 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             122.1              122.3 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             12.51              12.82 
[1] "0.1 - 122.1 (12.5)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         5        7       17       14        25        32
  17P LOSS WILD-TYPE       6       12       31       18        52        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED          13         36         32         14       19
  17P LOSS WILD-TYPE        16         61         40         34       32
                    vv
clus                 STAGE IVA
  17P LOSS MUTATED           1
  17P LOSS WILD-TYPE         3
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   5                  6
  STAGE IA                  7                 12
  STAGE IB                 17                 31
  STAGE II                 14                 18
  STAGE IIA                25                 52
  STAGE IIB                32                 52
  STAGE III                13                 16
  STAGE IIIA               36                 61
  STAGE IIIB               32                 40
  STAGE IIIC               14                 34
  STAGE IV                 19                 32
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17P LOSS MUTATED      17  46 117  39
  17P LOSS WILD-TYPE    36  80 163  85
D71V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               17                 36
  T2                  46                 80
  T3                 117                163
  T4                  39                 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"
                    vv
clus                  N0  N1  N2  N3
  17P LOSS MUTATED    73  66  41  36
  17P LOSS WILD-TYPE 127 116  55  61
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               73                127
  N1               66                116
  N2               41                 55
  N3               36                 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"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   193  12
  17P LOSS WILD-TYPE 320  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    193   12
  17P LOSS WILD-TYPE  320   27
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              193                320
  1               12                 27
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    59 170
  17P LOSS WILD-TYPE 123 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     59  170
  17P LOSS WILD-TYPE  123  257
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               59                123
  MALE                170                257
[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                                                 34
  17P LOSS WILD-TYPE                                               44
                    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                                34
  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                                  44
  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     4 225
  17P LOSS WILD-TYPE   2 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  225
  17P LOSS WILD-TYPE    2  378
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                  2
  YES              225                378
[1] 2 2
[1] FALSE
D71V10, continuous
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   130   9   6   5
  17P LOSS WILD-TYPE 217   9  13  20
D71V11, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              130                217
  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"
D71V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED      43                         4
  17P LOSS WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           1   142
  17P LOSS WILD-TYPE                                         0   243
D71V13, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                                   43                 86
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  142                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"
D71V14, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     3 131
  17P LOSS WILD-TYPE   4 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3  131
  17P LOSS WILD-TYPE    4  263
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              131                263
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    55  38
  17Q LOSS WILD-TYPE 299 183
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                93                482 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                38                183 
$`17Q LOSS MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A938 
        8.94         4.21         0.79        23.41        14.50        25.41 
TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A891 TCGA-LN-A49L TCGA-LN-A4A1 TCGA-R6-A6Y2 
        7.13         0.36         3.95        10.45        12.59         9.30 
TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EX 
       12.69         4.80         4.44        22.82        12.43        28.11 
TCGA-VR-A8Q7 TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-6458 
       42.87        10.16         2.66        11.01         6.61        19.33 
TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8296 
        9.17        35.24        18.71         0.69        16.31        15.58 
TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ 
       14.79         9.21         9.86        10.68         7.53        22.26 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-8524 
        0.72        13.51        20.65         1.15         3.25         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-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4477 
       20.02        54.08         4.01        47.05        19.07        30.97 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 
       11.93        20.55        17.19        10.26        15.22        11.31 
TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-FP-A8CX TCGA-HU-8245 
       14.66        11.31        15.65         7.99         0.23        12.59 
TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-IN-8663 TCGA-KB-A6F5 TCGA-KB-A93H 
       14.17        22.75         8.98         3.39         5.56        37.64 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
        9.86        45.67         8.61        16.67       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
        5.79         5.46        46.26        12.79        17.85         1.87 
TCGA-VQ-A8PX TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A94U TCGA-VQ-AA6B 
       64.57        18.74         9.50         9.73        22.09        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       54.12        21.11         0.79 

$`17Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       13.94        16.24        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30         0.53        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         4.67        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        42.77        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.43         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36         5.92        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35         0.10        13.25         0.10        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       10.52        12.00        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       33.11         5.16         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
       14.70         7.04        29.59         6.35        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         1.45         7.00        20.02        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET 
        3.42        15.35         9.27        18.81        19.96         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31         8.12        30.71        18.18        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       11.24         9.17        15.91         3.42         2.10        19.73 
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-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        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-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-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-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-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18        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-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       16.44        15.68         8.22        12.56        13.87         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-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        12.82         0.66        19.36         0.46        20.42 
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-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.10         3.42         9.34 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       12.43         6.58         0.10        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         7.99         8.05        14.01        29.98 
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-D7-6518 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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       17.85        13.35        15.98        12.79        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-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-A6F0 
       14.76        13.71        11.24        11.44         9.76         2.96 
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-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        0.56         5.52        18.08        26.47         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-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-A4GU 
       11.77        21.37        29.98         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-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-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-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73        18.21         8.52        61.25         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         9.24        11.05         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       19.04         0.92        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       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-A8PJ 
       28.96        34.29        16.31        22.19         2.50         2.70 
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-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-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z 
       20.81        22.68         1.71        36.16         7.36        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-AA64 
       64.18        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       40.08        28.41        32.94        17.13        26.04        16.14 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       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 
            11.610             12.905 
[1] "0.1 - 115.7 (11.6)" "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        7        6         9        16
  17Q LOSS WILD-TYPE      11       18       41       26        68        68
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           4         20         13          5        6
  17Q LOSS WILD-TYPE        25         77         59         43       45
                    vv
clus                 STAGE IVA
  17Q LOSS MUTATED           1
  17Q LOSS WILD-TYPE         3
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                 11
  STAGE IA                  1                 18
  STAGE IB                  7                 41
  STAGE II                  6                 26
  STAGE IIA                 9                 68
  STAGE IIB                16                 68
  STAGE III                 4                 25
  STAGE IIIA               20                 77
  STAGE IIIB               13                 59
  STAGE IIIC                5                 43
  STAGE IV                  6                 45
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17Q LOSS MUTATED       5  17  47  23
  17Q LOSS WILD-TYPE    48 109 233 101
D72V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                5                 48
  T2                  17                109
  T3                  47                233
  T4                  23                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
  17Q LOSS MUTATED    25  33  19  13
  17Q LOSS WILD-TYPE 175 149  77  84
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               25                175
  N1               33                149
  N2               19                 77
  N3               13                 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"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    85   3
  17Q LOSS WILD-TYPE 428  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     85    3
  17Q LOSS WILD-TYPE  428   36
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               85                428
  1                3                 36
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    31  66
  17Q LOSS WILD-TYPE 151 361
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     31   66
  17Q LOSS WILD-TYPE  151  361
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               31                151
  MALE                 66                361
[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                                                                  20
  17Q LOSS WILD-TYPE                                                                61
                    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)               20
  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)                 61
  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  96
  17Q LOSS WILD-TYPE   5 507
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   96
  17Q LOSS WILD-TYPE    5  507
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                  5
  YES               96                507
[1] 2 2
[1] FALSE
D72V10, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    59   3   3   4
  17Q LOSS WILD-TYPE 288  15  16  21
D72V11, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               59                288
  R1                3                 15
  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"
D72V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED      19                         1
  17Q LOSS WILD-TYPE   110                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           1    61
  17Q LOSS WILD-TYPE                                         0   324
D72V13, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                                   19                110
  BLACK OR AFRICAN AMERICAN                                1                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   61                324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3  62
  17Q LOSS WILD-TYPE   4 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   62
  17Q LOSS WILD-TYPE    4  332
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               62                332
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   114  61
  18P LOSS WILD-TYPE 240 160
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               175                400 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                61                160 
$`18P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        14.30         5.92         8.94        16.24        32.45 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       33.27         0.85         2.63         0.79        23.41        14.50 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       42.77        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       30.25         0.30        24.00         3.68         4.70        32.61 
TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE 
        7.17         7.43         6.94         2.60         3.95        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       13.22         8.71        52.57        10.36         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A4A1 TCGA-LN-A7HY TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.43        12.59        12.03         5.16         7.82         7.59 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
       29.59         6.35         9.30         1.45         7.00        20.02 
TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW TCGA-X8-AAAR TCGA-Z6-A8JD 
        9.27        19.96        18.31         8.12        10.16         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        2.66        19.73        19.56        11.01         9.47         9.44 
TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 
        9.57        17.29        13.68        26.10        12.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8289 TCGA-BR-8291 
       15.42        28.01        28.73         9.07         2.66        16.31 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8677 
       22.19         0.95        14.04        25.18        15.81         0.49 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
       11.54         9.86        15.68        10.68        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 
       22.26         1.48        12.89        13.18         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.10         0.13         0.10         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       11.31        12.43        11.61         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 
        4.01        47.05        19.07         7.07        30.97         1.02 
TCGA-CG-5732 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 
       69.04        19.13        20.55        18.54        13.35        15.98 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV 
       19.50        18.21        21.14        16.44        15.16        11.24 
TCGA-D7-A6EZ TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 
        9.76         0.62        72.23        11.38        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 
       22.29        17.06         0.23         1.51        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
       12.10        10.62        12.30        11.77         8.98         6.25 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A7NU 
        2.10        12.95         9.67         5.19         1.41         1.81 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
       13.51         5.56        20.15        37.64        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.52        16.67       115.69         5.79        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A91V 
       13.02        18.48        35.24        16.31         2.50        36.16 
TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA6B 
       52.24         4.54        64.18        42.54        22.09        29.98 
TCGA-VQ-AA6K 
       12.43 

$`18P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       31.27        58.55         7.63        13.94         4.21         7.69 
TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        6.21        20.09        20.78        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        4.67        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43J 
        3.68        41.52        25.41        21.70         6.28         4.31 
TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        8.94        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NM 
        8.71        25.12         0.36         7.40         3.02         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37        13.41        27.12        83.24        46.09 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.66        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25         0.10        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
       13.18         0.13        33.11         8.02         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW 
        7.04        53.95        15.78         2.89        12.69        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42         4.80        15.35         4.44        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       22.82        12.43         1.55        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
        2.10        26.70        11.70         6.61         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-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       15.95        13.87        19.33        39.12         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-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-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        12.43         3.45        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-8295 TCGA-BR-8296 
       20.55         8.05         0.56        12.95         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 
        7.40         6.18        19.50        13.08         0.26        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        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-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       15.81        16.44         8.22        12.56         6.08        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-5802 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 
       13.15         0.30         0.07         0.16         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10         3.42         9.34         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-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       18.97        12.00        22.98         6.97        36.00         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-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        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-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
        6.44         6.74        12.59         6.51         5.56         7.82 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZI 
        2.53        60.56         3.72        19.73         9.86        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-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-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV 
        8.94        35.61        16.87        19.04         0.92        13.25 
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-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.29        46.26        22.19        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-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-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58         5.72        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 

  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 
             12.59              12.79 
[1] "0.1 - 115.7 (12.6)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         3        5       10       10        23        22
  18P LOSS WILD-TYPE       8       14       38       22        54        62
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED          12         32         23         13       15
  18P LOSS WILD-TYPE        17         65         49         35       36
                    vv
clus                 STAGE IVA
  18P LOSS MUTATED           2
  18P LOSS WILD-TYPE         2
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  5                 14
  STAGE IB                 10                 38
  STAGE II                 10                 22
  STAGE IIA                23                 54
  STAGE IIB                22                 62
  STAGE III                12                 17
  STAGE IIIA               32                 65
  STAGE IIIB               23                 49
  STAGE IIIC               13                 35
  STAGE IV                 15                 36
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18P LOSS MUTATED      13  30  99  31
  18P LOSS WILD-TYPE    40  96 181  93
D73V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               13                 40
  T2                  30                 96
  T3                  99                181
  T4                  31                 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
  18P LOSS MUTATED    55  52  32  30
  18P LOSS WILD-TYPE 145 130  64  67
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               55                145
  N1               52                130
  N2               32                 64
  N3               30                 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"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   148  13
  18P LOSS WILD-TYPE 365  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    148   13
  18P LOSS WILD-TYPE  365   26
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              148                365
  1               13                 26
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    44 137
  18P LOSS WILD-TYPE 138 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     44  137
  18P LOSS WILD-TYPE  138  290
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               44                138
  MALE                137                290
[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                                                                  21
  18P LOSS WILD-TYPE                                                                60
                    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)               21
  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)                 60
  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     0 181
  18P LOSS WILD-TYPE   6 422
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0  181
  18P LOSS WILD-TYPE    6  422
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 0                  6
  YES              181                422
[1] 2 2
[1] FALSE
D73V10, continuous
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    93   5   4   4
  18P LOSS WILD-TYPE 254  13  15  21
D73V11, multiclass
    clus
vv   18P LOSS MUTATED 18P 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"
D73V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED      43                         4
  18P LOSS WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           0   113
  18P LOSS WILD-TYPE                                         1   272
D73V13, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                                   43                 86
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  113                272
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3 114
  18P LOSS WILD-TYPE   4 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3  114
  18P LOSS WILD-TYPE    4  280
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              114                280
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   151  88
  18Q LOSS WILD-TYPE 203 133
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               239                336 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                88                133 
$`18Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        31.27        14.30         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
        7.69         0.85         2.63         3.88         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FH 
       23.41         9.96        14.50        12.16        68.02        42.77 
TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       25.41        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.32         7.17         4.90        29.00         7.43         6.94 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR 
       12.92        13.48        16.47        13.55        13.22         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 
       10.45        12.66        12.43         0.10        13.25        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       22.39         0.10        12.33        13.22         4.47        12.33 
TCGA-LN-A7HX TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.23        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       29.59         6.35         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU 
       20.02         3.42         9.27        19.96        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD 
        8.12        46.19        15.06         9.17        10.16         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 
        9.44         6.61         6.18         9.57        17.29        13.68 
TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
       26.10        12.16        35.24        15.42        28.01        28.73 
TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 
        9.07        11.44        16.31        22.19         0.95        14.04 
TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 
        3.32        20.22        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-A4IY 
       15.68        10.68        13.87         7.53        22.26        12.89 
TCGA-BR-A4J6 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        0.66        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.10         0.13         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 
        3.42        12.43        11.61        12.20         3.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4466 
        8.05        54.08         4.01        47.05        19.07        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 
        7.07        22.98        30.97         1.02        12.03         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 
       69.04        12.36        19.13        20.55        18.54        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       17.19        10.26        15.98        19.50        18.21        14.66 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 
       21.14        16.44        15.16        11.24         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C 
       15.65         7.40         0.62         7.99        72.23        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8245 
       19.53        14.07        22.29        17.06         0.23        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-HU-A4GP 
       14.17        12.10        10.62        12.30        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-A6RL TCGA-IN-A6RO 
        6.25         2.10        12.95         9.67         5.19         1.41 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.74         5.56         1.81        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7C1 
       20.15        37.64        45.67        18.21         8.52        16.67 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       37.91       115.69         5.79        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A8PE 
       13.02        18.48        35.24         7.73        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91V TCGA-VQ-A91X 
        2.50        17.85        13.35        27.35        36.16         9.50 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T 
       52.24         2.01         4.54        64.18        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       22.09        32.94        29.98        12.43         0.79 

$`18Q LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RF 
       58.55         7.63         5.92        13.94         4.21         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       33.27        20.09        20.78        20.12        18.64         9.30 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
       17.03        12.82        14.86         4.67       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43E 
       60.39         3.68        41.52        21.70         6.28        30.25 
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        4.31        19.99        21.01        47.93        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        3.16        58.59         7.13         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NW TCGA-LN-A49O 
        7.40         7.76         5.49        21.37        46.09        13.41 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       13.15        15.35         0.10         0.10        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.76        12.59        15.52        11.54        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.00        12.03        13.18         0.13         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RB 
        7.04        53.95         9.30        15.78        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ET 
        4.80        15.35         4.44        18.81        22.82         1.55 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I 
       28.11        30.71        18.18        42.87        11.24        15.91 
TCGA-Z6-A8JE TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        2.10        26.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 
       30.90         6.61        34.68        15.95        13.87        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
        9.21        24.76        23.93        18.15        15.32        12.43 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        3.45        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-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 
       13.08         0.26        17.52        26.33         4.31        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-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21         1.12        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T 
        6.28         7.53        15.81        16.44         8.22        12.56 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        6.08         1.48        13.41        13.51         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17         0.53        12.82        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-8530 TCGA-CD-8531 TCGA-CD-8535 
        2.83         3.25        13.15         0.16         0.10         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-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 
       20.02        27.02        15.95         1.02        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5717 
       12.03        21.99         0.00         9.01        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
       36.00         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       28.96        79.07        65.10        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6817 
       11.93        18.84        18.61        17.85        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       10.55        11.31        12.33        24.72        16.80        17.19 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        14.27         5.92        13.78        14.76        13.71 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO 
       11.31        11.44         8.38         4.34         7.13        16.24 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.47        21.27         3.48        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        0.56         5.52        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       14.27        11.41         0.76        24.30         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10         6.51        10.19         0.26        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38         5.36        13.08         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ 
       12.59         6.51         7.82         2.53         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        9.86        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 

  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 
            12.330             13.115 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1"  
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         3        6       18       13        34        32
  18Q LOSS WILD-TYPE       8       13       30       19        43        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED          14         43         31         16       19
  18Q LOSS WILD-TYPE        15         54         41         32       32
                    vv
clus                 STAGE IVA
  18Q LOSS MUTATED           2
  18Q LOSS WILD-TYPE         2
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  6                 13
  STAGE IB                 18                 30
  STAGE II                 13                 19
  STAGE IIA                34                 43
  STAGE IIB                32                 52
  STAGE III                14                 15
  STAGE IIIA               43                 54
  STAGE IIIB               31                 41
  STAGE IIIC               16                 32
  STAGE IV                 19                 32
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18Q LOSS MUTATED      18  50 135  33
  18Q LOSS WILD-TYPE    35  76 145  91
D74V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               18                 35
  T2                  50                 76
  T3                 135                145
  T4                  33                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q LOSS MUTATED    78  76  40  38
  18Q LOSS WILD-TYPE 122 106  56  59
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               78                122
  N1               76                106
  N2               40                 56
  N3               38                 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"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   204  17
  18Q LOSS WILD-TYPE 309  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    204   17
  18Q LOSS WILD-TYPE  309   22
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              204                309
  1               17                 22
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    66 182
  18Q LOSS WILD-TYPE 116 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     66  182
  18Q LOSS WILD-TYPE  116  245
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               66                116
  MALE                182                245
[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                                                       52
  18Q LOSS WILD-TYPE                                                    110
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                                  33
  18Q LOSS WILD-TYPE                                                                48
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  18Q LOSS MUTATED                                                 33
  18Q LOSS WILD-TYPE                                               45
                    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)                          52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                33
  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)                           110
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  45
  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     1 247
  18Q LOSS WILD-TYPE   5 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1  247
  18Q LOSS WILD-TYPE    5  356
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 1                  5
  YES              247                356
[1] 2 2
[1] FALSE
D74V10, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   119   6   7   8
  18Q LOSS WILD-TYPE 228  12  12  17
D74V11, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              119                228
  R1                6                 12
  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"
D74V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED      56                         5
  18Q LOSS WILD-TYPE    73                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           0   154
  18Q LOSS WILD-TYPE                                         1   231
D74V13, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                                   56                 73
  BLACK OR AFRICAN AMERICAN                                5                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  154                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"
D74V14, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3 149
  18Q LOSS WILD-TYPE   4 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3  149
  18Q LOSS WILD-TYPE    4  245
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              149                245
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    93  73
  19P LOSS WILD-TYPE 261 148
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               166                409 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                73                148 
$`19P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30         7.63        16.24         4.21 
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
        2.63         3.88         0.53        17.03        23.41         9.96 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A938 TCGA-L5-A43E 
       14.50       122.10        68.02        42.77        25.41        30.25 
TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX 
        4.31         3.68        47.93         7.17        58.59         7.43 
TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
        3.95         2.66        16.47        13.55        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
        8.71        52.57        46.09        10.45        12.66         0.10 
TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       15.35        12.46        12.59        12.49        12.76         0.10 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6KZ 
        4.47        12.33        12.23        13.18         8.02         5.06 
TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8EZ 
        7.04        15.78         9.27        18.81         8.12        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TI 
       42.87        46.19         9.17         2.66        19.73        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 
       11.01         9.44         6.61        19.33         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-A4PF TCGA-CD-5799 TCGA-CD-5800 
       22.26         1.48         0.72         1.15         3.25        13.15 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
        0.07         0.07         0.07         3.42        11.31        12.43 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       12.20        20.02         7.99        54.08         4.01        29.98 
TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6520 TCGA-D7-6525 
       18.97        12.03        15.02        69.04        18.84        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A6EX 
       17.19        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-8099 
        2.96        15.65         0.62         7.99        72.23        17.06 
TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
        0.56         5.92        12.59        11.77         8.98         6.25 
TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 
        2.10        23.84        12.30         9.67        27.42         3.39 
TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 
       18.38         1.41        12.59         5.56         1.81         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A7BW 
       60.56        37.64        45.67        18.21         8.61         5.13 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       37.91         8.94         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PK TCGA-VQ-A8PM 
       13.02        18.48        35.24         7.73        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       27.35        18.74         1.71        36.16         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA6D 
       52.24         9.04         2.01        21.04        40.08        17.13 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       16.14        21.11        12.43         0.79 

$`19P LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE 
       58.55         5.92        13.94         8.94        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        6.21        33.27        20.09         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       18.64         9.30         0.79        12.82        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       12.16        44.75        60.39         3.68        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        0.30         8.94        24.00         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
       21.01        18.35         3.32         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         7.40         3.02        55.50        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.48         7.76        21.37        13.41        27.12        83.24 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V 
       10.36         5.92        12.43        13.41        13.15         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       13.25         0.10        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
       12.33        13.22        25.25        10.52        12.00        12.03 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 
        0.13        33.11         5.16         7.82         7.59        14.70 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
       29.59         6.35        53.95         9.30         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       12.69         7.00        20.02        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        4.80        15.35         4.44        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7B 
        1.55        18.31        28.11        30.71        15.06        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-5818 
       15.91        10.16         3.42         2.10        26.70        11.70 
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-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-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       17.29        13.68        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-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       15.42        18.15        15.32        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-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-8486 
        0.26        15.85         3.72         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        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-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
        8.22        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-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
       13.64        11.57         5.13         2.83        13.18         0.30 
TCGA-CD-5803 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-A487 TCGA-CD-A48C 
        0.10         0.13         0.13         0.10         9.34        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-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        1.02         8.05        14.01        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         0.00         9.01         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-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-D7-5578 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-D7-6528 TCGA-D7-6815 
       20.55        18.54        18.61        17.85        15.22        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-A4SO 
        9.76         8.38         4.34         7.40         7.13        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-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX 
       22.29        59.54         5.03        13.58         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-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-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
       29.98         0.10         6.51        10.19         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       19.36         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR 
        5.36         5.19        13.08         6.44         6.74         6.51 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
        7.82        13.51         2.53        20.15         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        9.86         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       11.05        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-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-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        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-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       20.81        22.68         7.36        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-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        32.94        29.98        54.12        26.04 
TCGA-ZA-A8F6 
       10.62 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             122.1              122.3 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            12.315             13.080 
[1] "0.1 - 122.1 (12.3)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1.3"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         3        7       12        7        24        25
  19P LOSS WILD-TYPE       8       12       36       25        53        59
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED          10         30         16         15       13
  19P LOSS WILD-TYPE        19         67         56         33       38
                    vv
clus                 STAGE IVA
  19P LOSS MUTATED           3
  19P LOSS WILD-TYPE         1
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  7                 12
  STAGE IB                 12                 36
  STAGE II                  7                 25
  STAGE IIA                24                 53
  STAGE IIB                25                 59
  STAGE III                10                 19
  STAGE IIIA               30                 67
  STAGE IIIB               16                 56
  STAGE IIIC               15                 33
  STAGE IV                 13                 38
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19P LOSS MUTATED      15  34  87  30
  19P LOSS WILD-TYPE    38  92 193  94
D75V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               15                 38
  T2                  34                 92
  T3                  87                193
  T4                  30                 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
  19P LOSS MUTATED    52  55  25  31
  19P LOSS WILD-TYPE 148 127  71  66
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               52                148
  N1               55                127
  N2               25                 71
  N3               31                 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"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   149  10
  19P LOSS WILD-TYPE 364  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    149   10
  19P LOSS WILD-TYPE  364   29
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              149                364
  1               10                 29
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    47 125
  19P LOSS WILD-TYPE 135 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     47  125
  19P LOSS WILD-TYPE  135  302
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               47                135
  MALE                125                302
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19P LOSS MUTATED                                       9
  19P LOSS WILD-TYPE                                    62
                    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                                            9
  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                                             62
  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     2 170
  19P LOSS WILD-TYPE   4 433
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2  170
  19P LOSS WILD-TYPE    4  433
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 2                  4
  YES              170                433
[1] 2 2
[1] FALSE
D75V10, continuous
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    91   2   6   3
  19P LOSS WILD-TYPE 256  16  13  22
D75V11, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               91                256
  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"
D75V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED      42                         5
  19P LOSS WILD-TYPE    87                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           1    98
  19P LOSS WILD-TYPE                                         0   287
D75V13, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                                   42                 87
  BLACK OR AFRICAN AMERICAN                                5                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   98                287
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1 100
  19P LOSS WILD-TYPE   6 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1  100
  19P LOSS WILD-TYPE    6  294
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              100                294
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    78  49
  19Q LOSS WILD-TYPE 276 172
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               127                448 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                49                172 
$`19Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-IG-A3YB TCGA-IG-A50L 
       25.78        31.27        14.30         4.21         2.63         0.53 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH 
       23.41         9.96        14.50       122.10        68.02        42.77 
TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OS 
       25.41        30.25         4.31        47.93         7.17        58.59 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NR 
        7.43         6.94         3.95         2.66        13.22         8.71 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 
       10.45        12.66         0.10        13.15        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-R6-A6DN 
       12.49         4.47        12.33        12.23        13.18         8.02 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 
       15.78         1.45        18.81         8.12        18.18        42.87 
TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        9.17         2.66        19.73        11.01         9.44         6.61 
TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 
        9.17        35.24        28.73        11.44         0.69         2.66 
TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8678 TCGA-BR-A4CS TCGA-BR-A4PF 
        2.20        14.04        14.79        11.54         1.48         1.15 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A489 
        3.25        13.15         0.07         0.07         3.42        11.31 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4443 
       12.43        12.20        20.02         7.99         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6526 
       19.07        18.97        12.03        15.02        69.04        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A6EX 
       10.26        15.22        12.79        11.31        19.50        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 
        2.96        15.65         0.62        17.06         0.56         5.92 
TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H5 
       12.59        11.77         8.98         6.25        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT 
        9.67        27.42        18.38         1.41        12.59         5.56 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BW 
        1.81         5.56        37.64        45.67        18.21         5.13 
TCGA-RD-A8MW TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       37.91        48.79         5.46        13.02        18.48        35.24 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X 
       17.85         1.87        27.35        18.74        36.16         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J 
       52.24         9.04        21.04        17.13        16.14        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`19Q LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       32.45         7.69         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
       20.78        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA 
        0.79        12.82        14.86         4.67        12.16        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       60.39         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M 
       25.22        24.03         6.28         3.16         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.13         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
       13.55         7.76         5.49        21.37        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       83.24        52.57        46.09        10.36         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 
       13.41        15.35         0.10        13.25         0.10        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO 
       13.22        25.25        10.52        12.00        12.03         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         5.16         7.82         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
        7.04        29.59         6.35        53.95         9.30         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       12.69         7.00        20.02        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D 
       12.43         1.55        18.31        28.11        30.71        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.06        11.24        15.91        10.16         3.42         2.10 
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-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83        13.18         0.30         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-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.13         0.10         9.34        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-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
        8.05        54.08        14.01        47.05        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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
      105.07        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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       18.84        18.54        18.61        17.85        13.35        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 
             122.1              122.3 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            12.430             12.905 
[1] "0.1 - 122.1 (12.4)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         3        6       10        6        20        18
  19Q LOSS WILD-TYPE       8       13       38       26        57        66
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           6         22         14          9       11
  19Q LOSS WILD-TYPE        23         75         58         39       40
                    vv
clus                 STAGE IVA
  19Q LOSS MUTATED           2
  19Q LOSS WILD-TYPE         2
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   3                  8
  STAGE IA                  6                 13
  STAGE IB                 10                 38
  STAGE II                  6                 26
  STAGE IIA                20                 57
  STAGE IIB                18                 66
  STAGE III                 6                 23
  STAGE IIIA               22                 75
  STAGE IIIB               14                 58
  STAGE IIIC                9                 39
  STAGE IV                 11                 40
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19Q LOSS MUTATED      11  28  68  21
  19Q LOSS WILD-TYPE    42  98 212 103
D76V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1               11                 42
  T2                  28                 98
  T3                  68                212
  T4                  21                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
  19Q LOSS MUTATED    46  37  19  23
  19Q LOSS WILD-TYPE 154 145  77  74
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               46                154
  N1               37                145
  N2               19                 77
  N3               23                 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"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   113   9
  19Q LOSS WILD-TYPE 400  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    113    9
  19Q LOSS WILD-TYPE  400   30
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0              113                400
  1                9                 30
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    37  95
  19Q LOSS WILD-TYPE 145 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     37   95
  19Q LOSS WILD-TYPE  145  332
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               37                145
  MALE                 95                332
[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                                                       27
  19Q LOSS WILD-TYPE                                                    135
                    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                                                 23
  19Q LOSS WILD-TYPE                                               55
                    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)                          27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                23
  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)                           135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  55
  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     1 131
  19Q LOSS WILD-TYPE   5 472
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1  131
  19Q LOSS WILD-TYPE    5  472
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 1                  5
  YES              131                472
[1] 2 2
[1] FALSE
D76V10, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    71   0   4   3
  19Q LOSS WILD-TYPE 276  18  15  22
D76V11, 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"
D76V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED      36                         4
  19Q LOSS WILD-TYPE    93                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           0    70
  19Q LOSS WILD-TYPE                                         1   315
D76V13, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                                   36                 93
  BLACK OR AFRICAN AMERICAN                                4                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   70                315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  78
  19Q LOSS WILD-TYPE   6 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   78
  19Q LOSS WILD-TYPE    6  316
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               78                316
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    23  15
  20P LOSS WILD-TYPE 331 206
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                38                537 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                206 
$`20P LOSS MUTATED`
TCGA-2H-A9GI TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OF 
       14.30        44.75        68.02        42.77         8.94         3.68 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NL TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O 
       32.61         3.32        13.22        83.24        12.66        13.41 
TCGA-LN-A49Y TCGA-LN-A7HW TCGA-LN-A7HY TCGA-R6-A6XG TCGA-S8-A6BW TCGA-VR-A8EQ 
       12.46        12.00        12.03        29.59        20.38        22.82 
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-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       12.16       122.10        60.39         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
        3.16        30.25         0.30         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        5.92        10.45        12.43         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.25         0.10        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        10.52        12.23 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        14.70         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.02         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       15.06        11.24         9.17        15.91        10.16         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-6458 TCGA-BR-6563 TCGA-BR-6565 
       15.95        13.87        13.68        19.33        39.12         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-8291 
        9.60        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-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-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-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51         0.46        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-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-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-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-D7-5579 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-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        19.50        17.19        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-8122 TCGA-F1-6874 
        8.38         4.34         7.40         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-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-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.19        13.08         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         5.56         1.81        13.51         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-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-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-A91E TCGA-VQ-A91K 
       64.57        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        22.68         1.71        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-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-AA69 TCGA-VQ-AA6A 
       42.54        11.24        22.09        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 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.62               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             83.24             122.30 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            14.235             12.660 
[1] "0.6 - 83.2 (14.2)"  "0.0 - 122.3 (12.7)"
[1] "hr=" "1.1"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         1        2        4        0         6         5
  20P LOSS WILD-TYPE      10       17       44       32        71        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           4          5          5          2        4
  20P LOSS WILD-TYPE        25         92         67         46       47
                    vv
clus                 STAGE IVA
  20P LOSS MUTATED           0
  20P LOSS WILD-TYPE         4
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   1                 10
  STAGE IA                  2                 17
  STAGE IB                  4                 44
  STAGE II                  0                 32
  STAGE IIA                 6                 71
  STAGE IIB                 5                 79
  STAGE III                 4                 25
  STAGE IIIA                5                 92
  STAGE IIIB                5                 67
  STAGE IIIC                2                 46
  STAGE IV                  4                 47
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20P LOSS MUTATED       5  10  18   6
  20P LOSS WILD-TYPE    48 116 262 118
D77V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                5                 48
  T2                  10                116
  T3                  18                262
  T4                   6                118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P LOSS MUTATED    14  11   8   6
  20P LOSS WILD-TYPE 186 171  88  91
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               14                186
  N1               11                171
  N2                8                 88
  N3                6                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    30   3
  20P LOSS WILD-TYPE 483  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     30    3
  20P LOSS WILD-TYPE  483   36
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               30                483
  1                3                 36
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    13  27
  20P LOSS WILD-TYPE 169 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     13   27
  20P LOSS WILD-TYPE  169  400
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               13                169
  MALE                 27                400
[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  38
  20P LOSS WILD-TYPE   4 565
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   38
  20P LOSS WILD-TYPE    4  565
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 2                  4
  YES               38                565
[1] 2 2
[1] FALSE
D77V10, continuous
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    18   1   2   1
  20P LOSS WILD-TYPE 329  17  17  24
D77V11, 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"
D77V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED       9                         1
  20P LOSS WILD-TYPE   120                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           0    25
  20P LOSS WILD-TYPE                                         1   360
D77V13, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                                    9                120
  BLACK OR AFRICAN AMERICAN                                1                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   25                360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  22
  20P LOSS WILD-TYPE   7 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   22
  20P LOSS WILD-TYPE    7  372
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               22                372
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     5   2
  20Q LOSS WILD-TYPE 349 219
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                568 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                219 
$`20Q LOSS MUTATED`
TCGA-JY-A6FA TCGA-JY-A6FH TCGA-L5-A43M TCGA-LN-A7HW TCGA-S8-A6BW TCGA-VR-A8EQ 
       44.75        42.77         8.94        12.00        20.38        22.82 
TCGA-IN-A6RJ 
        5.36 

$`20Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.02         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       15.06        11.24         9.17        15.91        10.16         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-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-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-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-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-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        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-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-D7-5579 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-D7-6817 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-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-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-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         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-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-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38         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-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-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-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-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-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-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        22.68         1.71        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-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 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              5.36               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             44.75             122.30 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             20.38              12.76 
[1] "5.4 - 44.8 (20.4)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.8"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         0        0        2        0         1         3
  20Q LOSS WILD-TYPE      11       19       46       32        76        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           1          0          0          0        0
  20Q LOSS WILD-TYPE        28         97         72         48       51
                    vv
clus                 STAGE IVA
  20Q LOSS MUTATED           0
  20Q LOSS WILD-TYPE         4
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                 11
  STAGE IA                  0                 19
  STAGE IB                  2                 46
  STAGE II                  0                 32
  STAGE IIA                 1                 76
  STAGE IIB                 3                 81
  STAGE III                 1                 28
  STAGE IIIA                0                 97
  STAGE IIIB                0                 72
  STAGE IIIC                0                 48
  STAGE IV                  0                 51
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20Q LOSS MUTATED       1   5   2   0
  20Q LOSS WILD-TYPE    52 121 278 124
D78V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                1                 52
  T2                   5                121
  T3                   2                278
  T4                   0                124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q LOSS MUTATED     3   4   1   0
  20Q LOSS WILD-TYPE 197 178  95  97
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                3                197
  N1                4                178
  N2                1                 95
  N3                0                 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"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   0
  20Q LOSS WILD-TYPE 507  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    0
  20Q LOSS WILD-TYPE  507   39
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                6                507
  1                0                 39
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   7
  20Q LOSS WILD-TYPE 181 420
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    7
  20Q LOSS WILD-TYPE  181  420
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                181
  MALE                  7                420
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                    71
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20Q LOSS MUTATED                                                        1
  20Q LOSS WILD-TYPE                                                    161
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20Q LOSS MUTATED                                                                   0
  20Q LOSS WILD-TYPE                                                                81
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  20Q LOSS MUTATED                                                  0
  20Q LOSS WILD-TYPE                                               78
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  20Q LOSS MUTATED                                                          0
  20Q LOSS WILD-TYPE                                                       21
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  20Q LOSS MUTATED                                                           0
  20Q LOSS WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  20Q LOSS MUTATED                                          0
  20Q LOSS WILD-TYPE                                       13
D78V8, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                433 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-B7-A5TI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B7-A5TJ         TCGA-B7-A5TK         TCGA-B7-A5TN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4183         TCGA-BR-4184         TCGA-BR-4187 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4188         TCGA-BR-4191         TCGA-BR-4201 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4257         TCGA-BR-4267         TCGA-BR-4279 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4292         TCGA-BR-4294 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4357         TCGA-BR-4361         TCGA-BR-4362 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4363         TCGA-BR-4366         TCGA-BR-4367 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4368         TCGA-BR-4369         TCGA-BR-4370 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4371         TCGA-BR-6452         TCGA-BR-6453 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6454         TCGA-BR-6455         TCGA-BR-6456 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6457         TCGA-BR-6458         TCGA-BR-6563 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6564         TCGA-BR-6565         TCGA-BR-6566 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6705         TCGA-BR-6706         TCGA-BR-6707 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6709         TCGA-BR-6710         TCGA-BR-6801 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6802         TCGA-BR-6803         TCGA-BR-6852 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7196         TCGA-BR-7197         TCGA-BR-7703 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7704         TCGA-BR-7707         TCGA-BR-7715 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7716         TCGA-BR-7717         TCGA-BR-7722 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7723         TCGA-BR-7851         TCGA-BR-7901 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7957         TCGA-BR-7958         TCGA-BR-7959 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8058         TCGA-BR-8059         TCGA-BR-8060 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8360         TCGA-BR-8361         TCGA-BR-8362 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8363         TCGA-BR-8364         TCGA-BR-8365 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8366         TCGA-BR-8367         TCGA-BR-8368 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8369         TCGA-BR-8370         TCGA-BR-8371 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8372         TCGA-BR-8373         TCGA-BR-8380 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8381         TCGA-BR-8382         TCGA-BR-8384 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8483         TCGA-BR-8484         TCGA-BR-8485 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8486         TCGA-BR-8487         TCGA-BR-8588 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8589         TCGA-BR-8590         TCGA-BR-8591 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-8676         TCGA-BR-8677 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8678         TCGA-BR-8679         TCGA-BR-8680 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8682         TCGA-BR-8683         TCGA-BR-8686 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8687         TCGA-BR-8690         TCGA-BR-A44T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A44U         TCGA-BR-A452         TCGA-BR-A453 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4CQ         TCGA-BR-A4CR         TCGA-BR-A4CS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4IU         TCGA-BR-A4IV         TCGA-BR-A4IY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4IZ         TCGA-BR-A4J1         TCGA-BR-A4J2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4J4         TCGA-BR-A4J5         TCGA-BR-A4J6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4J7         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4PD         TCGA-BR-A4PE         TCGA-BR-A4PF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4QI         TCGA-BR-A4QL         TCGA-BR-A4QM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-5804         TCGA-CD-8524         TCGA-CD-8525 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-8526         TCGA-CD-8527         TCGA-CD-8528 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-8529         TCGA-CD-8530         TCGA-CD-8531 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-8532         TCGA-CD-8533         TCGA-CD-8534 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-8535         TCGA-CD-8536         TCGA-CD-A486 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-A487         TCGA-CD-A489         TCGA-CD-A48A 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-A48C         TCGA-CD-A4MG         TCGA-CD-A4MH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-A4MI         TCGA-CD-A4MJ         TCGA-CG-4300 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4442         TCGA-CG-4443         TCGA-CG-4444 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4474         TCGA-CG-4476 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-8570         TCGA-D7-8572         TCGA-D7-8573 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-8574         TCGA-D7-8575         TCGA-D7-8576 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-8578         TCGA-D7-8579         TCGA-D7-A4YT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A4YU         TCGA-D7-A4YV         TCGA-D7-A4YX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A4YY         TCGA-D7-A4Z0         TCGA-D7-A6ET 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A6EV         TCGA-D7-A6EX         TCGA-D7-A6EY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A6EZ         TCGA-D7-A6F0         TCGA-D7-A6F2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A747         TCGA-D7-A748         TCGA-D7-A74A 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A74B         TCGA-EQ-5647         TCGA-EQ-8122 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EQ-A4SO         TCGA-F1-6177         TCGA-F1-6874 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F1-6875         TCGA-F1-A448         TCGA-F1-A72C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-8210         TCGA-FP-8211         TCGA-FP-8631 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-A4BF         TCGA-FP-A8CX         TCGA-HF-7131 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HF-7132         TCGA-HF-7133         TCGA-HF-7134 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HF-7136         TCGA-HF-A5NB         TCGA-HJ-7597 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-8238         TCGA-HU-8243         TCGA-HU-8244 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-8245         TCGA-HU-8249         TCGA-HU-8602 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-8604         TCGA-HU-8608         TCGA-HU-8610 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4G2         TCGA-HU-A4G3         TCGA-HU-A4G6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4G8         TCGA-HU-A4G9         TCGA-HU-A4GC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GD         TCGA-HU-A4GF         TCGA-HU-A4GH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GJ         TCGA-HU-A4GN         TCGA-HU-A4GP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GQ         TCGA-HU-A4GT         TCGA-HU-A4GU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GX         TCGA-HU-A4GY         TCGA-HU-A4H0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4H2         TCGA-HU-A4H3         TCGA-HU-A4H4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4H5         TCGA-HU-A4H6         TCGA-HU-A4H8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4HB         TCGA-HU-A4HD         TCGA-IN-7806 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IN-8462         TCGA-IN-8663 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-A6RI         TCGA-IN-A6RL         TCGA-IN-A6RN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-A6RO         TCGA-IN-A6RP         TCGA-IN-A6RR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-A6RS         TCGA-IN-A7NR         TCGA-IN-A7NT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-A7NU         TCGA-IN-AB1V         TCGA-IN-AB1X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IP-7968         TCGA-KB-A6F5         TCGA-KB-A6F7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KB-A93G         TCGA-KB-A93H         TCGA-MX-A5UG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MX-A5UJ         TCGA-MX-A663         TCGA-R5-A7O7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-R5-A7ZE         TCGA-R5-A7ZF         TCGA-R5-A7ZI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-R5-A7ZR         TCGA-R5-A804         TCGA-R5-A805 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A7BS         TCGA-RD-A7BT         TCGA-RD-A7BW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A7C1         TCGA-RD-A8MV         TCGA-RD-A8MW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8N0         TCGA-RD-A8N1         TCGA-RD-A8N2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8N4         TCGA-RD-A8N5         TCGA-RD-A8N6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8N9         TCGA-RD-A8NB         TCGA-SW-A7EA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-SW-A7EB         TCGA-VQ-A8DL         TCGA-VQ-A8DT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8DU         TCGA-VQ-A8DV         TCGA-VQ-A8DZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8E0         TCGA-VQ-A8E2         TCGA-VQ-A8E3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8E7         TCGA-VQ-A8P2         TCGA-VQ-A8P3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8P5         TCGA-VQ-A8P8         TCGA-VQ-A8PB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PC         TCGA-VQ-A8PD         TCGA-VQ-A8PE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PF         TCGA-VQ-A8PH         TCGA-VQ-A8PJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PK         TCGA-VQ-A8PM         TCGA-VQ-A8PO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PP         TCGA-VQ-A8PQ         TCGA-VQ-A8PS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PT         TCGA-VQ-A8PU         TCGA-VQ-A8PX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PY         TCGA-VQ-A8PZ         TCGA-VQ-A91A 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91D         TCGA-VQ-A91E         TCGA-VQ-A91K 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91N         TCGA-VQ-A91Q         TCGA-VQ-A91S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91U         TCGA-VQ-A91V         TCGA-VQ-A91W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91X         TCGA-VQ-A91Y         TCGA-VQ-A91Z 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A922         TCGA-VQ-A923         TCGA-VQ-A924 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A925         TCGA-VQ-A927         TCGA-VQ-A928 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A92D         TCGA-VQ-A94O         TCGA-VQ-A94P 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A94R         TCGA-VQ-A94T         TCGA-VQ-A94U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA64         TCGA-VQ-AA68         TCGA-VQ-AA69 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA6A         TCGA-VQ-AA6B         TCGA-VQ-AA6D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA6F         TCGA-VQ-AA6G         TCGA-VQ-AA6I 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA6J         TCGA-VQ-AA6K         TCGA-ZA-A8F6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ZQ-A9CR 
"20Q LOSS WILD-TYPE" 
D78V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   8
  20Q LOSS WILD-TYPE   6 595
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    8
  20Q LOSS WILD-TYPE    6  595
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 0                  6
  YES                8                595
[1] 2 2
[1] FALSE
D78V10, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     1   0   0   0
  20Q LOSS WILD-TYPE 346  18  19  25
D78V11, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                408 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-4183 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4184         TCGA-BR-4187         TCGA-BR-4188 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4191         TCGA-BR-4201         TCGA-BR-4253 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4256         TCGA-BR-4257 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4267         TCGA-BR-4279         TCGA-BR-4280 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4292         TCGA-BR-4294         TCGA-BR-4357 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4361         TCGA-BR-4362         TCGA-BR-4363 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4366         TCGA-BR-4367         TCGA-BR-4368 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4369         TCGA-BR-4370         TCGA-BR-4371 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6452         TCGA-BR-6453         TCGA-BR-6454 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6456         TCGA-BR-6457 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6458         TCGA-BR-6563         TCGA-BR-6564 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-BR-7196 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7197         TCGA-BR-7703         TCGA-BR-7704 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7707         TCGA-BR-7715         TCGA-BR-7716 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7717         TCGA-BR-7722         TCGA-BR-7723 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7851         TCGA-BR-7901         TCGA-BR-7957 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7958         TCGA-BR-7959         TCGA-BR-8058 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8059         TCGA-BR-8060         TCGA-BR-8077 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8078         TCGA-BR-8080         TCGA-BR-8081 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8284         TCGA-BR-8285         TCGA-BR-8286 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8289         TCGA-BR-8291         TCGA-BR-8295 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8296         TCGA-BR-8297         TCGA-BR-8360 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8361         TCGA-BR-8362         TCGA-BR-8363 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8364         TCGA-BR-8365         TCGA-BR-8366 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8367         TCGA-BR-8368         TCGA-BR-8369 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8370         TCGA-BR-8371         TCGA-BR-8372 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8373         TCGA-BR-8380         TCGA-BR-8381 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8382         TCGA-BR-8384         TCGA-BR-8483 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8484         TCGA-BR-8485         TCGA-BR-8486 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8487         TCGA-BR-8588         TCGA-BR-8589 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8590         TCGA-BR-8591         TCGA-BR-8592 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8676         TCGA-BR-8677         TCGA-BR-8678 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8679         TCGA-BR-8680         TCGA-BR-8682 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8683         TCGA-BR-8686         TCGA-BR-8687 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8690         TCGA-BR-A44T         TCGA-BR-A44U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A452         TCGA-BR-A453         TCGA-BR-A4CQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4CR         TCGA-BR-A4CS         TCGA-BR-A4IU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4IV         TCGA-BR-A4IY         TCGA-BR-A4IZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4J1         TCGA-BR-A4J2         TCGA-BR-A4J4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4J5         TCGA-BR-A4J6         TCGA-BR-A4J7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4J8         TCGA-BR-A4J9         TCGA-BR-A4PD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4PE         TCGA-BR-A4PF         TCGA-BR-A4QI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4QL         TCGA-BR-A4QM         TCGA-CD-5800 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5804         TCGA-CD-8524 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-8525         TCGA-CD-8526         TCGA-CD-8527 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-8528         TCGA-CD-8529         TCGA-CD-8530 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-8531         TCGA-CD-8532         TCGA-CD-8533 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-8534         TCGA-CD-8535         TCGA-CD-8536 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-A487         TCGA-CG-4300         TCGA-CG-4301 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4442 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4475 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-4477         TCGA-CG-5716 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-D7-8570         TCGA-D7-8572 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-8573         TCGA-D7-8574         TCGA-D7-8575 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-8576         TCGA-D7-8578         TCGA-D7-8579 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A4YT         TCGA-D7-A4YU         TCGA-D7-A4YV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A4YX         TCGA-D7-A4YY         TCGA-D7-A4Z0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A6ET         TCGA-D7-A6EV         TCGA-D7-A6EX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A6EY         TCGA-D7-A6EZ         TCGA-D7-A6F0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A6F2         TCGA-D7-A747         TCGA-D7-A748 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A74A         TCGA-D7-A74B         TCGA-EQ-5647 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EQ-A4SO         TCGA-F1-6177         TCGA-F1-6874 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F1-6875         TCGA-F1-A448         TCGA-F1-A72C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8211 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-FP-A4BF         TCGA-FP-A8CX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HF-7131         TCGA-HF-7132         TCGA-HF-7133 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HF-7134         TCGA-HF-7136         TCGA-HF-A5NB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HJ-7597         TCGA-HU-8238         TCGA-HU-8243 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-8244         TCGA-HU-8245         TCGA-HU-8249 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-8602         TCGA-HU-8604         TCGA-HU-8608 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-8610         TCGA-HU-A4G2         TCGA-HU-A4G3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4G6         TCGA-HU-A4G9         TCGA-HU-A4GC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GD         TCGA-HU-A4GF         TCGA-HU-A4GH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GJ         TCGA-HU-A4GN         TCGA-HU-A4GP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GQ         TCGA-HU-A4GT         TCGA-HU-A4GU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GX         TCGA-HU-A4GY         TCGA-HU-A4H0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4H2         TCGA-HU-A4H3         TCGA-HU-A4H4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4H5         TCGA-HU-A4H6         TCGA-HU-A4H8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4HB         TCGA-HU-A4HD         TCGA-IN-7806 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-8462         TCGA-IN-8663         TCGA-IN-A6RI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-A6RL         TCGA-IN-A6RN         TCGA-IN-A6RO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-A6RP         TCGA-IN-A6RR         TCGA-IN-A6RS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-A7NR         TCGA-IN-A7NT         TCGA-IN-A7NU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-AB1V         TCGA-IN-AB1X         TCGA-IP-7968 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KB-A6F5         TCGA-KB-A6F7         TCGA-KB-A93G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KB-A93H         TCGA-MX-A5UG         TCGA-MX-A5UJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MX-A663         TCGA-R5-A7ZI         TCGA-RD-A7BS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A7BT         TCGA-RD-A7BW         TCGA-RD-A7C1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8MV         TCGA-RD-A8MW         TCGA-RD-A8N0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8N1         TCGA-RD-A8N2         TCGA-RD-A8N4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8N5         TCGA-RD-A8N6         TCGA-RD-A8N9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8NB         TCGA-SW-A7EA         TCGA-SW-A7EB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8DL         TCGA-VQ-A8DT         TCGA-VQ-A8DU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8DV         TCGA-VQ-A8DZ         TCGA-VQ-A8E0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8E2         TCGA-VQ-A8E3         TCGA-VQ-A8E7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8P2         TCGA-VQ-A8P3         TCGA-VQ-A8P5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8P8         TCGA-VQ-A8PB         TCGA-VQ-A8PC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PD         TCGA-VQ-A8PE         TCGA-VQ-A8PF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PH         TCGA-VQ-A8PJ         TCGA-VQ-A8PK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PM         TCGA-VQ-A8PO         TCGA-VQ-A8PP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PQ         TCGA-VQ-A8PS         TCGA-VQ-A8PT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PU         TCGA-VQ-A8PX         TCGA-VQ-A8PY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PZ         TCGA-VQ-A91A         TCGA-VQ-A91D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91E         TCGA-VQ-A91K         TCGA-VQ-A91N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91Q         TCGA-VQ-A91S         TCGA-VQ-A91U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91V         TCGA-VQ-A91W         TCGA-VQ-A91X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91Y         TCGA-VQ-A91Z         TCGA-VQ-A922 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A923         TCGA-VQ-A924         TCGA-VQ-A925 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A927         TCGA-VQ-A928         TCGA-VQ-A92D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A94O         TCGA-VQ-A94P         TCGA-VQ-A94R 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A94T         TCGA-VQ-A94U         TCGA-VQ-AA64 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA68         TCGA-VQ-AA69         TCGA-VQ-AA6A 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA6B         TCGA-VQ-AA6D         TCGA-VQ-AA6F 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA6G         TCGA-VQ-AA6I         TCGA-VQ-AA6J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA6K         TCGA-ZA-A8F6         TCGA-ZQ-A9CR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D78V12, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                386 
        TCGA-B7-5816         TCGA-B7-A5TI         TCGA-BR-4183 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4184         TCGA-BR-4188         TCGA-BR-4191 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4267         TCGA-BR-4279         TCGA-BR-4280 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4361         TCGA-BR-4362         TCGA-BR-4367 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-4368         TCGA-BR-6452         TCGA-BR-6453 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6454         TCGA-BR-6455         TCGA-BR-6456 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6457         TCGA-BR-6458         TCGA-BR-6563 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6564         TCGA-BR-6565         TCGA-BR-6566 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6705         TCGA-BR-6706         TCGA-BR-6707 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6709         TCGA-BR-6710         TCGA-BR-6801 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-6802         TCGA-BR-6803         TCGA-BR-6852 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7196         TCGA-BR-7197         TCGA-BR-7703 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7704         TCGA-BR-7707         TCGA-BR-7715 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7716         TCGA-BR-7717         TCGA-BR-7722 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7723         TCGA-BR-7851         TCGA-BR-7901 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-7957         TCGA-BR-7958         TCGA-BR-7959 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8058         TCGA-BR-8059         TCGA-BR-8060 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8360         TCGA-BR-8361         TCGA-BR-8362 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8363         TCGA-BR-8364         TCGA-BR-8365 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8366         TCGA-BR-8367         TCGA-BR-8368 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8369         TCGA-BR-8370         TCGA-BR-8371 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8372         TCGA-BR-8373         TCGA-BR-8380 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8381         TCGA-BR-8382         TCGA-BR-8384 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8483         TCGA-BR-8484         TCGA-BR-8485 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8486         TCGA-BR-8487         TCGA-BR-8588 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8589         TCGA-BR-8590         TCGA-BR-8591 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-8676         TCGA-BR-8677 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8678         TCGA-BR-8679         TCGA-BR-8680 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8682         TCGA-BR-8683         TCGA-BR-8686 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-8687         TCGA-BR-8690         TCGA-BR-A44T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A44U         TCGA-BR-A452         TCGA-BR-A453 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4CQ         TCGA-BR-A4CR         TCGA-BR-A4CS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4IU         TCGA-BR-A4IV         TCGA-BR-A4IY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4IZ         TCGA-BR-A4J1         TCGA-BR-A4J2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4J4         TCGA-BR-A4J5         TCGA-BR-A4J6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4J8         TCGA-BR-A4J9         TCGA-BR-A4PD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4PE         TCGA-BR-A4PF         TCGA-BR-A4QI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BR-A4QL         TCGA-BR-A4QM         TCGA-CD-5804 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-8525         TCGA-CD-8526         TCGA-CD-8531 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CD-8535         TCGA-CD-A487         TCGA-CG-4301 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4436 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4442         TCGA-CG-4443 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4460         TCGA-CG-4462         TCGA-CG-4465 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4475         TCGA-CG-4476 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5717         TCGA-CG-5718 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-D7-8570 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-8572         TCGA-D7-8573         TCGA-D7-8574 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-8575         TCGA-D7-8576         TCGA-D7-8578 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-8579         TCGA-D7-A4YT         TCGA-D7-A4YU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A4YV         TCGA-D7-A4YX         TCGA-D7-A4YY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A4Z0         TCGA-D7-A6ET         TCGA-D7-A6EV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A6EX         TCGA-D7-A6EY         TCGA-D7-A6EZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A6F0         TCGA-D7-A6F2         TCGA-D7-A747 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D7-A748         TCGA-D7-A74A         TCGA-D7-A74B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-EQ-A4SO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F1-A448         TCGA-F1-A72C         TCGA-FP-7735 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-8211         TCGA-FP-8631         TCGA-FP-A4BF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FP-A8CX         TCGA-HF-7131         TCGA-HF-7132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HF-7133         TCGA-HF-7134         TCGA-HF-7136 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HF-A5NB         TCGA-HJ-7597         TCGA-HU-8238 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-8243         TCGA-HU-8244         TCGA-HU-8245 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-8249         TCGA-HU-8602         TCGA-HU-8604 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-8608         TCGA-HU-8610         TCGA-HU-A4G2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4G3         TCGA-HU-A4G6         TCGA-HU-A4G8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4G9         TCGA-HU-A4GC         TCGA-HU-A4GD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GF         TCGA-HU-A4GH         TCGA-HU-A4GJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GN         TCGA-HU-A4GP         TCGA-HU-A4GQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GT         TCGA-HU-A4GU         TCGA-HU-A4GX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4GY         TCGA-HU-A4H0         TCGA-HU-A4H2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4H3         TCGA-HU-A4H4         TCGA-HU-A4H5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4H6         TCGA-HU-A4H8         TCGA-HU-A4HB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HU-A4HD         TCGA-IN-7806         TCGA-IN-7808 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-8462         TCGA-IN-8663         TCGA-IN-A6RI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-A6RL         TCGA-IN-A6RN         TCGA-IN-A6RO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-A6RP         TCGA-IN-A6RR         TCGA-IN-A6RS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-A7NR         TCGA-IN-A7NT         TCGA-IN-A7NU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IN-AB1V         TCGA-IN-AB1X         TCGA-IP-7968 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KB-A6F5         TCGA-KB-A6F7         TCGA-KB-A93G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KB-A93H         TCGA-MX-A5UG         TCGA-MX-A5UJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MX-A663         TCGA-R5-A7ZI         TCGA-RD-A7BS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A7BT         TCGA-RD-A7BW         TCGA-RD-A7C1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8MV         TCGA-RD-A8MW         TCGA-RD-A8N0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8N1         TCGA-RD-A8N2         TCGA-RD-A8N4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8N5         TCGA-RD-A8N6         TCGA-RD-A8N9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RD-A8NB         TCGA-SW-A7EA         TCGA-SW-A7EB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8DL         TCGA-VQ-A8DT         TCGA-VQ-A8DU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8DV         TCGA-VQ-A8DZ         TCGA-VQ-A8E0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8E2         TCGA-VQ-A8E3         TCGA-VQ-A8E7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8P2         TCGA-VQ-A8P3         TCGA-VQ-A8P5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8P8         TCGA-VQ-A8PB         TCGA-VQ-A8PC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PD         TCGA-VQ-A8PE         TCGA-VQ-A8PF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PH         TCGA-VQ-A8PJ         TCGA-VQ-A8PK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PM         TCGA-VQ-A8PO         TCGA-VQ-A8PP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PQ         TCGA-VQ-A8PS         TCGA-VQ-A8PT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PU         TCGA-VQ-A8PX         TCGA-VQ-A8PY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A8PZ         TCGA-VQ-A91A         TCGA-VQ-A91D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91E         TCGA-VQ-A91K         TCGA-VQ-A91N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91Q         TCGA-VQ-A91S         TCGA-VQ-A91U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91V         TCGA-VQ-A91W         TCGA-VQ-A91X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A91Y         TCGA-VQ-A91Z         TCGA-VQ-A922 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A923         TCGA-VQ-A924         TCGA-VQ-A925 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A927         TCGA-VQ-A928         TCGA-VQ-A92D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A94O         TCGA-VQ-A94R         TCGA-VQ-A94T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-A94U         TCGA-VQ-AA64         TCGA-VQ-AA68 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA69         TCGA-VQ-AA6A         TCGA-VQ-AA6B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA6D         TCGA-VQ-AA6F         TCGA-VQ-AA6G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VQ-AA6I         TCGA-VQ-AA6J         TCGA-VQ-AA6K 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ZA-A8F6         TCGA-ZQ-A9CR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20Q LOSS MUTATED       3                         0
  20Q LOSS WILD-TYPE   126                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q LOSS MUTATED                                           0     4
  20Q LOSS WILD-TYPE                                         1   381
D78V13, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                                    3                126
  BLACK OR AFRICAN AMERICAN                                0                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                381
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   4
  20Q LOSS WILD-TYPE   7 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    4
  20Q LOSS WILD-TYPE    7  390
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                4                390
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   159 108
  21Q LOSS WILD-TYPE 195 113
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               267                308 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               108                113 
$`21Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR 
       25.78         7.63         5.92        13.94         8.94        32.45 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A93C TCGA-JY-A93D 
        0.53         0.79         9.96       122.10        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       25.22        24.03         3.16        30.25         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        8.94        24.00         4.70        32.61        21.01        47.93 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        7.43         6.94         2.60         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W 
        5.92        12.43        13.41         0.10        13.15        13.25 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW 
       12.76         0.10        12.33        13.22        12.33        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.23        12.03        13.18        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE 
        9.30         2.89         1.45        12.69         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        18.81        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
        8.12        28.11        18.18        42.87        46.19        11.24 
TCGA-VR-AA7D TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ 
        9.17         2.10         2.66        19.73        11.70        11.01 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
        9.44         6.97        18.35        13.68        19.33        26.10 
TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
        9.17        31.20        35.24        15.42        28.01        28.73 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 
       18.71        14.43        11.44         9.60         8.05        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 
       15.58         7.40        19.50        17.52         4.31        14.04 
TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 
       14.79         5.39        25.18         9.21        11.54         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       15.68        10.68         7.53        22.26         1.48         0.72 
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-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8535 
        0.07         0.07         0.07         0.10         0.16         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 
       11.31        12.43        11.61        12.20        20.02        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
        4.01        47.05        12.03        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        6.97         1.02        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       69.04        11.93        19.13        13.35        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX 
       12.79        11.31        14.66        21.14        16.44        11.31 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 
       15.65         7.40         0.62        72.23        11.38        19.53 
TCGA-FP-8099 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
       17.06         0.23        26.47         1.51        14.17        12.10 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H3 
       11.84         3.25         8.98         6.25         0.26        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       23.84        12.30         9.67        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NR 
       18.38         5.36         5.19         1.41         6.74         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.56         1.81         7.82         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       20.15        37.64         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 
       61.25         6.08         9.24       122.30        37.91       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       13.25        18.48         7.73        22.19        17.85         1.87 
TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91K 
       23.41        27.35        64.57        14.33        36.69        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A91Z 
       18.74        20.81         1.71        36.16         9.73        52.24 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        2.01        55.43         4.54        21.04        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       22.09        18.41        40.08        29.98        17.13        54.12 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       21.11        12.43         0.79 

$`21Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
       31.27        14.30        58.55        16.24         4.21         7.69 
TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
        6.21        20.09         2.63         9.30        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO 
       21.70         6.28         3.68        19.99        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI 
        1.38         8.71        25.12        55.50        35.97        13.48 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
        7.76         5.49        21.37        83.24        10.45        12.66 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35         0.10         0.10        12.46        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59        22.39        15.52        11.54         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A9FO TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO 
       10.52         0.13        14.70        53.95        15.78         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU 
       20.02        20.38         5.29        15.35        19.96        18.31 
TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-B7-5816 
       30.71        15.06        15.91        10.16         3.42        26.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       19.56         9.47         6.61         4.64         7.43        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-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       17.29        39.12        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        21.11        30.90        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
        9.21        24.76        23.93        18.15        15.32        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 
        3.45         9.07        12.76        17.49         0.69        12.26 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 
       20.55         0.56        12.95         2.66         2.20         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 
       13.08         0.26        22.19         0.95        26.33         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
       11.80        19.17         0.26        15.85         3.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T 
        7.53         0.49        15.81        16.44         8.22        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       13.87         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-A4QL 
       14.17         0.53        12.82         0.66        19.36        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-8525 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.13         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         3.42         9.34         6.58         0.10        12.62 
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-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        21.99         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        7.07        12.00        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
      105.07        28.96        79.07        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       10.26        15.22        10.55        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       19.50        17.19        18.21        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
        9.76         2.96         8.38         4.34         7.13         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       16.24        14.47        21.27         3.48        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         5.52        18.08 
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-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        12.30        24.20        22.75        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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
        2.10        12.95         8.88         8.81        27.42         3.45 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-AB1X TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.08         6.44        12.59        13.51         3.72        19.73 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        4.60        11.05         8.61         5.13        16.67        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8DZ 
      116.38        71.38        16.87        19.04         5.46        13.02 
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-A8PJ 
       34.29        46.26        16.31         2.50        12.79         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D 
        9.27        15.65        13.35        26.24        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A927 
       11.93        22.68         7.36         9.50         9.04         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6G 
        5.72        64.18         2.66        28.41        32.94        26.04 
TCGA-VQ-AA6I TCGA-ZA-A8F6 
       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 
             12.43              12.82 
[1] "0.1 - 122.3 (12.4)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1"  
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         7        7       24        9        32        34
  21Q LOSS WILD-TYPE       4       12       24       23        45        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED          18         51         31         21       20
  21Q LOSS WILD-TYPE        11         46         41         27       31
                    vv
clus                 STAGE IVA
  21Q LOSS MUTATED           2
  21Q LOSS WILD-TYPE         2
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   7                  4
  STAGE IA                  7                 12
  STAGE IB                 24                 24
  STAGE II                  9                 23
  STAGE IIA                32                 45
  STAGE IIB                34                 50
  STAGE III                18                 11
  STAGE IIIA               51                 46
  STAGE IIIB               31                 41
  STAGE IIIC               21                 27
  STAGE IV                 20                 31
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  21Q LOSS MUTATED      23  54 135  48
  21Q LOSS WILD-TYPE    30  72 145  76
D79V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               23                 30
  T2                  54                 72
  T3                 135                145
  T4                  48                 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"
                    vv
clus                  N0  N1  N2  N3
  21Q LOSS MUTATED    84  86  47  41
  21Q LOSS WILD-TYPE 116  96  49  56
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               84                116
  N1               86                 96
  N2               47                 49
  N3               41                 56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   232  14
  21Q LOSS WILD-TYPE 281  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    232   14
  21Q LOSS WILD-TYPE  281   25
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              232                281
  1               14                 25
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    86 193
  21Q LOSS WILD-TYPE  96 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     86  193
  21Q LOSS WILD-TYPE   96  234
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               86                 96
  MALE                193                234
[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                                                 37
  21Q LOSS WILD-TYPE                                               41
                    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
D79V8, 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                                37
  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                                  41
  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"
D79V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4 275
  21Q LOSS WILD-TYPE   2 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4  275
  21Q LOSS WILD-TYPE    2  328
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                  2
  YES              275                328
[1] 2 2
[1] FALSE
D79V10, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   145   7   6   8
  21Q LOSS WILD-TYPE 202  11  13  17
D79V11, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              145                202
  R1                7                 11
  R2                6                 13
  RX                8                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED      50                         7
  21Q LOSS WILD-TYPE    79                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           0   179
  21Q LOSS WILD-TYPE                                         1   206
D79V13, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                                   50                 79
  BLACK OR AFRICAN AMERICAN                                7                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  179                206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4 161
  21Q LOSS WILD-TYPE   3 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4  161
  21Q LOSS WILD-TYPE    3  233
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              161                233
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   114  88
  22Q LOSS WILD-TYPE 240 133
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               202                373 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                88                133 
$`22Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YB 
       13.94         8.94        16.24         4.21        32.45         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 
       18.64         3.88         0.53         0.79        23.41         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A4OE 
      122.10        42.77        25.41        31.56         3.16        24.00 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        4.70        32.61        58.59         4.90        29.00         7.13 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        0.36         7.40         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR 
       13.48        16.47        13.55        13.22         5.49         8.71 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R 
       46.09        10.36         5.92        10.45        13.41         0.10 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HV TCGA-LN-A7HY 
       15.35        13.25         0.10        12.76        10.52        12.03 
TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W5 
       13.18         8.02         7.59         5.06        29.59        15.78 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO 
        2.89         7.00         5.29         4.80         9.27        18.81 
TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TJ 
       22.82        18.31         2.10         2.66        19.73        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 
        9.44         6.61         6.18        17.29        19.33        26.10 
TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-8058 
        9.17        12.16         9.21        15.42        28.01        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8369 
       14.43        11.44         0.69         9.60         7.40        14.04 
TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
       25.18         0.49        11.54        16.44         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF 
       10.68        22.26         0.72        19.36        20.65         1.15 
TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.64        13.15         0.30         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.16         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 
       11.61        12.20         8.05        54.08         4.01        47.05 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 
       21.99        18.97        30.97        12.03        15.02        69.04 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       12.66        11.93        20.55        10.26        15.22        12.79 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX 
       11.31        19.50        18.21        21.14        16.44        11.31 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-FP-7829 TCGA-FP-8099 
       15.65         7.40         0.62        16.24        19.53        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP 
        0.56         5.52         5.92        14.17        22.75         8.98 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 
        0.26         2.10        23.84         9.67        27.42         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU 
       18.38         5.36        13.08         6.44         6.74         1.81 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A663 TCGA-R5-A7O7 
        7.82         2.53         5.56        20.15         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 
       18.21         6.08         8.61        16.67       115.69        35.61 
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-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       18.48        46.26        22.19        12.79        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       27.35        14.33        36.69        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-A94U 
       36.16         9.50         9.73        64.18        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       18.41        32.94        29.98         0.79 

$`22Q LOSS WILD-TYPE`
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       20.12         9.30        17.03        12.82         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        23.18        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI 
       30.25         0.30         4.31         8.94         3.68        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        3.16         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
        3.95        35.97         7.76        21.37        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49V 
       83.24        52.57        12.66        12.43        13.15         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       25.25        12.00        12.23         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.82        14.70         7.04         6.35        53.95         9.30 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
        1.45        12.69        20.02        20.38         3.42        15.35 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
        4.44        19.96        12.43         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-5818 
        9.17        15.91        10.16         3.42        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       13.68        39.12        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-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        35.24        23.93        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8078 
       12.43         3.45         9.07        12.76        18.71        12.26 
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-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-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-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8686 
        9.34        13.45         6.28         7.53        15.81        15.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         7.53         6.08         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-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        13.51         0.46        20.42        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8528 
        2.83         3.25        13.18         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG 
        0.13         0.10         0.10         0.13         0.10         6.58 
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-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        1.02         7.99        14.01        29.98        19.07        12.03 
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-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-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       13.35        17.19        15.98        10.55        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       16.80        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-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
        9.76         2.96         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-7916 
       14.47        72.23        21.27        11.38         3.48        14.07 
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-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        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-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51         6.25        10.19        12.95        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-A6RL TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X 
        5.19         1.41        12.59         6.51         5.56        13.51 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       60.56        37.64         3.72        19.73         8.52        61.25 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         9.24        11.05         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       19.04        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
        7.73        28.96        34.29        16.31         2.50         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        26.24        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W 
       65.16        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-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA69 
        5.72        21.04         2.66        42.54        40.08        28.41 
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 
       10.62 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.07               0.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             122.1              122.3 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            12.315             12.820 
[1] "0.1 - 122.1 (12.3)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         6        1       18       11        23        28
  22Q LOSS WILD-TYPE       5       18       30       21        54        56
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED          18         35         26         15       16
  22Q LOSS WILD-TYPE        11         62         46         33       35
                    vv
clus                 STAGE IVA
  22Q LOSS MUTATED           3
  22Q LOSS WILD-TYPE         1
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   6                  5
  STAGE IA                  1                 18
  STAGE IB                 18                 30
  STAGE II                 11                 21
  STAGE IIA                23                 54
  STAGE IIB                28                 56
  STAGE III                18                 11
  STAGE IIIA               35                 62
  STAGE IIIB               26                 46
  STAGE IIIC               15                 33
  STAGE IV                 16                 35
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  22Q LOSS MUTATED      20  39 111  33
  22Q LOSS WILD-TYPE    33  87 169  91
D80V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1               20                 33
  T2                  39                 87
  T3                 111                169
  T4                  33                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q LOSS MUTATED    62  66  36  35
  22Q LOSS WILD-TYPE 138 116  60  62
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               62                138
  N1               66                116
  N2               36                 60
  N3               35                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   182  12
  22Q LOSS WILD-TYPE 331  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    182   12
  22Q LOSS WILD-TYPE  331   27
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              182                331
  1               12                 27
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    59 153
  22Q LOSS WILD-TYPE 123 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     59  153
  22Q LOSS WILD-TYPE  123  274
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               59                123
  MALE                153                274
[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                                                 32
  22Q LOSS WILD-TYPE                                               46
                    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
D80V8, 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                                32
  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                                  46
  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"
D80V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     4 208
  22Q LOSS WILD-TYPE   2 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4  208
  22Q LOSS WILD-TYPE    2  395
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 4                  2
  YES              208                395
[1] 2 2
[1] FALSE
D80V10, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED   109   8   7   6
  22Q LOSS WILD-TYPE 238  10  12  19
D80V11, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              109                238
  R1                8                 10
  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"
D80V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED      42                         3
  22Q LOSS WILD-TYPE    87                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           1   132
  22Q LOSS WILD-TYPE                                         0   253
D80V13, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                                   42                 87
  BLACK OR AFRICAN AMERICAN                                3                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  132                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"
D80V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     2 128
  22Q LOSS WILD-TYPE   5 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2  128
  22Q LOSS WILD-TYPE    5  266
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              128                266
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    73  39
  XP LOSS WILD-TYPE 281 182
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              112               463 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               39               182 
$`XP LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YA 
       25.78        14.30         4.21        32.45        20.09        20.78 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        3.88         0.53        23.41        12.82         9.96         4.67 
TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OE 
       44.75        42.77        25.41        23.18        30.25        24.00 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ 
       21.01        18.35         7.17         3.95        13.48        16.47 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R 
        8.71        13.41        46.09         5.92        12.66         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 
       12.46        12.59        22.39        11.54        13.22        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ 
       10.52        12.00         0.13        33.11         8.02         5.06 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        1.45        12.69        20.02         4.80         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-Z6-A8JD 
       18.81        18.31         8.12        42.87        15.91         3.42 
TCGA-Z6-A8JE TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-8059 
        2.10        19.56         9.44        18.35        19.33        14.43 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8680 TCGA-BR-8683 
       16.31         7.40        19.50        13.08        15.81         9.86 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8535 TCGA-CD-A489 
       13.87        22.26        13.64         0.07         0.13        11.31 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       12.20        20.02         3.02        29.98        47.05        19.07 
TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        7.07        15.02        11.93        15.22        15.98        12.79 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       12.33        18.21        11.31         9.76         2.96        15.65 
TCGA-D7-A74A TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4H5 
        7.40        13.58         5.52        12.10        22.75        12.30 
TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
       21.21         3.39        18.38         5.19         6.44         6.74 
TCGA-R5-A7O7 TCGA-VQ-A8PC TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91Z TCGA-VQ-A92D 
       45.67        46.26        13.35        27.35        52.24        64.18 
TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       22.09        40.08        32.94        17.13 

$`XP LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB 
       16.24         7.69         6.21        33.27         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A7DP 
       20.12        18.64         9.30        17.03         0.79        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         0.30         4.31         8.94         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       32.61        19.99        47.93         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
        8.71         2.60        25.12         0.36         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        35.97        12.92        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        27.12        83.24        52.57 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.36        10.45        12.43        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        13.25         0.10        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX 
        0.10        15.52        12.33         4.47        12.33        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.03        13.18         5.16         7.82         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        2.89         7.00        20.38         5.29         3.42        15.35 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96        22.82        12.43         1.55        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       18.18        46.19        15.06        11.24         9.17        10.16 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        11.01         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-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-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-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-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-8295 TCGA-BR-8296 TCGA-BR-8360 
        0.56        12.95         2.66         2.20        15.58         6.18 
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-8687 
        7.53         0.49        11.54        16.44        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        12.56         7.53         6.08         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-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-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        6.58         0.10        12.62        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-A747 TCGA-D7-A748 TCGA-D7-A74B 
       13.71        11.24        11.44         8.38         4.34         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-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       59.54         5.03         0.56         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-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-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-A6RN 
        8.81        27.42         3.45        18.81         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        1.41        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-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-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        28.96        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        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-A922 
        1.71        36.16         7.36         9.50         9.73         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-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        42.54        11.24        18.41        28.41        29.98 
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 

  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 
            13.53             12.56 
[1] "0.1 - 64.2 (13.5)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1.2"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         3        2        9        3        18        19
  XP LOSS WILD-TYPE       8       17       39       29        59        65
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           9         22         10          7        5
  XP LOSS WILD-TYPE        20         75         62         41       46
                   vv
clus                STAGE IVA
  XP LOSS MUTATED           0
  XP LOSS WILD-TYPE         4
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  3                 8
  STAGE IA                 2                17
  STAGE IB                 9                39
  STAGE II                 3                29
  STAGE IIA               18                59
  STAGE IIB               19                65
  STAGE III                9                20
  STAGE IIIA              22                75
  STAGE IIIB              10                62
  STAGE IIIC               7                41
  STAGE IV                 5                46
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XP LOSS MUTATED       9  27  56  17
  XP LOSS WILD-TYPE    44  99 224 107
D81V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1               9                44
  T2                 27                99
  T3                 56               224
  T4                 17               107
[1] 4 2
[1] 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    42  38  19   9
  XP LOSS WILD-TYPE 158 144  77  88
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              42               158
  N1              38               144
  N2              19                77
  N3               9                88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   101   4
  XP LOSS WILD-TYPE 412  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    101    4
  XP LOSS WILD-TYPE  412   35
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0             101               412
  1               4                35
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    20  96
  XP LOSS WILD-TYPE 162 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     20   96
  XP LOSS WILD-TYPE  162  331
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              20               162
  MALE                96               331
[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                                                       20
  XP LOSS WILD-TYPE                                                    142
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XP LOSS MUTATED                                                                   8
  XP LOSS WILD-TYPE                                                                73
                   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
D81V8, multiclass
                                                                   clus
vv                                                                  XP LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               8
  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)                          142
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                73
  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"
D81V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     1 115
  XP LOSS WILD-TYPE   5 488
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1  115
  XP LOSS WILD-TYPE    5  488
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                1                 5
  YES             115               488
[1] 2 2
[1] FALSE
D81V10, continuous
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    47   4   1   2
  XP LOSS WILD-TYPE 300  14  18  23
D81V11, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              47               300
  R1               4                14
  R2               1                18
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XP LOSS MUTATED      30                         0
  XP LOSS WILD-TYPE    99                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP LOSS MUTATED                                           0    72
  XP LOSS WILD-TYPE                                         1   313
D81V13, multiclass
                                           clus
vv                                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                                  30                99
  BLACK OR AFRICAN AMERICAN                               0                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  72               313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2  73
  XP LOSS WILD-TYPE   5 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   73
  XP LOSS WILD-TYPE    5  321
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              73               321
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    57  33
  XQ LOSS WILD-TYPE 297 188
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               90               485 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               33               188 
$`XQ LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A625 TCGA-JY-A6FH TCGA-JY-A938 
       25.78         4.21        32.45        12.82        42.77        25.41 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
       30.25        24.00        21.01        18.35         7.17         3.16 
TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L5-A8NW TCGA-LN-A49R 
        3.95        13.48        16.47         8.71        46.09         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 
       12.46        12.59        22.39        11.54        13.22        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A8WC 
       10.52        12.00        33.11         8.02         5.06         1.45 
TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       12.69         3.42         4.80         9.27         4.44        18.81 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-A5TI TCGA-B7-A5TN 
        8.12        42.87         3.42         2.10        19.56         9.44 
TCGA-BR-4191 TCGA-BR-7197 TCGA-BR-8059 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8678 
       18.35         9.21        14.43        16.31        19.50        11.54 
TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4QI TCGA-CD-8524 
       15.81        13.87        22.26         1.48        13.64         0.07 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4443 
        0.13        11.31        20.02         3.02         7.99        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6519 
       47.05        19.07         7.07        15.02        11.93        20.55 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6EZ 
       12.79        12.33        18.21        14.66        11.31         9.76 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-8604 TCGA-HU-A4H5 
        2.96         7.40        13.58         5.52        12.10        12.30 
TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR TCGA-VQ-A8E0 
       21.21         3.39        18.38         6.44         6.74        18.48 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91Q TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6D 
       13.35        27.35        20.81        22.09        32.94        17.13 

$`XQ LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       60.39        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        4.31         8.94         3.68         4.70        32.61        19.99 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93         3.32         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        13.25         0.10        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX 
        0.10        15.52        12.33         4.47        12.33        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.03        13.18         0.13         5.16         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         7.00        20.02        20.38         5.29 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       15.35        19.96        22.82        12.43         1.55        18.31 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        30.71        18.18        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        9.17        15.91        10.16         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.70        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        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-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-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82        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-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        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-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         7.40         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-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-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        0.49        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56         7.53         6.08        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-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-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.30         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-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
        0.10        12.62        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       54.08         4.01        14.01        12.03        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97        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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        12.36        12.66        19.13        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-D7-8570 TCGA-D7-8572 
       15.22        15.98        10.55        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        17.19        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-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       11.44        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 
           12.805            12.760 
[1] "0.1 - 47.0 (12.8)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D82V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         3        3        8        4        13        10
  XQ LOSS WILD-TYPE       8       16       40       28        64        74
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           7         17          8          5        5
  XQ LOSS WILD-TYPE        22         80         64         43       46
                   vv
clus                STAGE IVA
  XQ LOSS MUTATED           0
  XQ LOSS WILD-TYPE         4
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  3                 8
  STAGE IA                 3                16
  STAGE IB                 8                40
  STAGE II                 4                28
  STAGE IIA               13                64
  STAGE IIB               10                74
  STAGE III                7                22
  STAGE IIIA              17                80
  STAGE IIIB               8                64
  STAGE IIIC               5                43
  STAGE IV                 5                46
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XQ LOSS MUTATED       9  21  43  12
  XQ LOSS WILD-TYPE    44 105 237 112
D82V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1               9                44
  T2                 21               105
  T3                 43               237
  T4                 12               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
  XQ LOSS MUTATED    33  26  15  10
  XQ LOSS WILD-TYPE 167 156  81  87
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              33               167
  N1              26               156
  N2              15                81
  N3              10                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"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    79   2
  XQ LOSS WILD-TYPE 434  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     79    2
  XQ LOSS WILD-TYPE  434   37
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              79               434
  1               2                37
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    16  77
  XQ LOSS WILD-TYPE 166 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     16   77
  XQ LOSS WILD-TYPE  166  350
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              16               166
  MALE                77               350
[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                                                       19
  XQ LOSS WILD-TYPE                                                    143
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                                  10
  XQ LOSS WILD-TYPE                                                                71
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XQ LOSS MUTATED                                                 11
  XQ LOSS WILD-TYPE                                               67
                   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
D82V8, multiclass
                                                                   clus
vv                                                                  XQ LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               11
  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)                          143
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                71
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 67
  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"
D82V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  91
  XQ LOSS WILD-TYPE   4 512
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   91
  XQ LOSS WILD-TYPE    4  512
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                2                 4
  YES              91               512
[1] 2 2
[1] FALSE
D82V10, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    42   5   1   2
  XQ LOSS WILD-TYPE 305  13  18  23
D82V11, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              42               305
  R1               5                13
  R2               1                18
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED      18                         2
  XQ LOSS WILD-TYPE   111                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           0    57
  XQ LOSS WILD-TYPE                                         1   328
D82V13, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                                  18               111
  BLACK OR AFRICAN AMERICAN                               2                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  57               328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1  56
  XQ LOSS WILD-TYPE   6 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   56
  XQ LOSS WILD-TYPE    6  338
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              56               338
[1] 2 2
[1] FALSE
