[1] "ofn"        "-oTPRAD-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/PRAD-TP/15087329/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/15098599/transformed.cor.cli.txt"

nPatients in clinical file=489, in cluster file=492, common to both=482
[1] "Reduce the number of clustering variables from 82 to 80."
[1]  80 482
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               16               466 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               16               466 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25               457 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25               457 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               472 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               472 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7               475 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7               475 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               38               444 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               38               444 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               52               430 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               52               430 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               474 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               474 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               472 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               472 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23               459 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23               459 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               470 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               470 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                9               473 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                9               473 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5               477 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5               477 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               99               383 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               99               383 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               92               390 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               92               390 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               70               412 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               70               412 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              121               361 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              121               361 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               31               451 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               31               451 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               47               435 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               47               435 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                468 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                468 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                469 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                469 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                24                458 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                24                458 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                455 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                455 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                13                469 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                13                469 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                466 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                466 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                474 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                474 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                473 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                473 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                476 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                476 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                30                452 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                30                452 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                474 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                474 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                475 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                475 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                10                472 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                10                472 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                465 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                465 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                474 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                474 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                471 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                471 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                471 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                471 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                24                458 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                24                458 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                27                455 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                27                455 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                20                462 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                20                462 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                478 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                478 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6               476 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6               476 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6               476 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6               476 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               461 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               461 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6               476 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6               476 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               467 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               467 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               464 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               464 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9               473 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9               473 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5               477 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5               477 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               459 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               459 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16               466 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16               466 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12               470 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12               470 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               22               460 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               22               460 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               23               459 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               23               459 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               37               445 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               37               445 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              162               320 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              162               320 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               23               459 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               23               459 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               20               462 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               20               462 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                9               473 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                9               473 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                40                442 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                40                442 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                41                441 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                41                441 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                475 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                475 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                477 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                477 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                47                435 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                47                435 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                19                463 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                19                463 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                75                407 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                75                407 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                457 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                457 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                36                446 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                36                446 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                30                452 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                30                452 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               102                380 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               102                380 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                73                409 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                73                409 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                463 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                463 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                415 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                415 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                98                384 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                98                384 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                465 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                465 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                465 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                465 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                464 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                464 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                474 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                474 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                23                459 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                23                459 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                437 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                437 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               37               445 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               37               445 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               37               445 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               37               445 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "COMPLETENESS_OF_RESECTION"             
[17] "NUMBER_OF_LYMPH_NODES"                 
[18] "GLEASON_SCORE_COMBINED"                
[19] "GLEASON_SCORE_PRIMARY"                 
[20] "GLEASON_SCORE_SECONDARY"               
[21] "HIGHEST_GLEASON_SCORE"                 
[22] "GLEASON_SCORE"                         
[23] "PSA_RESULT_PREOP"                      
[24] "DAYS_TO_PREOP_PSA"                     
[25] "PSA_VALUE"                             
[26] "DAYS_TO_PSA"                           
[27] "RACE"                                  
[28] "ETHNICITY"                             
[29] "BATCH_NUMBER"                          

Input Data has 29 rows and 482 columns.

[1] "Batch" "29"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=8,	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=427,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=13,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE_COMBINED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'GLEASON_SCORE_PRIMARY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE_SECONDARY':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'HIGHEST_GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HIGHEST_GLEASON_SCORE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 22:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'PSA_RESULT_PREOP':	nDistinctValues=207,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'DAYS_TO_PREOP_PSA':	nDistinctValues=203,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 25:'PSA_VALUE':	nDistinctValues=109,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'DAYS_TO_PSA':	nDistinctValues=375,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 27:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 28:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 29:'BATCH_NUMBER':	nDistinctValues=22,	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] "****** SUMMARY ***** "
Output Data has 482 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"            "PATHOLOGY_T_STAGE"        
 [3] "PATHOLOGY_N_STAGE"         "HISTOLOGICAL_TYPE"        
 [5] "COMPLETENESS_OF_RESECTION" "NUMBER_OF_LYMPH_NODES"    
 [7] "GLEASON_SCORE_COMBINED"    "GLEASON_SCORE_PRIMARY"    
 [9] "GLEASON_SCORE_SECONDARY"   "GLEASON_SCORE"            
[11] "PSA_RESULT_PREOP"          "PSA_VALUE"                
[13] "RACE"                     
YEARS_TO_BIRTH, nv=36, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T2  T3  T4 
188 281  10 
[1] "table(vv)"
vv
 T2  T3  T4 
188 281  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T2  T3  T4 
188 281  10 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
188 281  10 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=12, binary=FALSE, numeric=TRUE
GLEASON_SCORE_COMBINED, nv=6, binary=FALSE, numeric=TRUE
GLEASON_SCORE_PRIMARY, nv=5, binary=FALSE, numeric=TRUE
GLEASON_SCORE_SECONDARY, nv=4, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_RESULT_PREOP, nv=207, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=109, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    16   0
  1P GAIN WILD-TYPE 457   8
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               16               465 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                 8 
$`1P GAIN MUTATED`
TCGA-CH-5766 TCGA-EJ-5518 TCGA-EJ-7788 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6499 
        1.02        52.27        14.14        15.42        13.45        50.73 
TCGA-J4-AATZ TCGA-J9-A52E TCGA-J9-A8CM TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-VP-A875 
       13.55        10.62        15.22        58.39        79.73        75.91 
TCGA-XK-AAIV TCGA-YL-A8HM TCGA-YL-A8SR TCGA-ZG-A9L5 
       37.25        48.72         8.98        29.85 

$`1P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       60.23        46.55        47.80        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 
       38.37        25.87        25.68        20.55        14.53        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V 
        4.54         4.31         4.77        28.41        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 
       25.15        27.29        58.22        56.75        64.18        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP 
       27.12        13.87         5.85        13.32        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O9 
       52.08        30.38        15.58        22.55         6.64         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      111.39       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        53.36        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       51.45        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI 
       32.45       114.38        71.34        62.79        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.02              0.72 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            79.73            165.17 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           22.635            26.660 
[1] "1.0 - 79.7 (22.6)"  "0.7 - 165.2 (26.7)"
[1] "hr="     "2.6e+07"
D1V2, continuous
                   vv
clus                 T2  T3  T4
  1P GAIN MUTATED     0  13   3
  1P GAIN WILD-TYPE 188 268   7
D1V3, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T2               0               188
  T3              13               268
  T4               3                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    10   5
  1P GAIN WILD-TYPE 328  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     10    5
  1P GAIN WILD-TYPE  328   70
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              10               328
  1               5                70
[1] 2 2
[1] FALSE
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  16
  1P GAIN WILD-TYPE  14 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   16
  1P GAIN WILD-TYPE   14  452
                                        clus
vv                                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 16               452
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED     6   9   0   0
  1P GAIN WILD-TYPE 304 129   5  15
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               6               304
  R1               9               129
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, continuous
D1V8, continuous
D1V9, continuous
D1V10, continuous
D1V11, continuous
D1V12, continuous
D1V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         0     5
  1P GAIN WILD-TYPE     2                         7   141
D1V14, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   5               141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    25   0
  1Q GAIN WILD-TYPE 448   8
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25               456 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 8 
$`1Q GAIN MUTATED`
TCGA-CH-5766 TCGA-EJ-5518 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-FC-7961 TCGA-FC-A4JI 
        1.02        52.27        25.68        14.14        15.42        13.45 
TCGA-G9-6362 TCGA-G9-6499 TCGA-HI-7168 TCGA-J4-AATZ TCGA-J9-A52E TCGA-J9-A8CM 
       47.44        50.73        78.61        13.55        10.62        15.22 
TCGA-KK-A8I4 TCGA-M7-A725 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-VN-A88K TCGA-VN-A88Q 
       67.99        18.84        58.39        79.73        25.51        44.91 
TCGA-VP-A875 TCGA-XK-AAIV TCGA-YL-A8HM TCGA-YL-A8SR TCGA-ZG-A9L5 TCGA-ZG-A9LZ 
       75.91        37.25        48.72         8.98        29.85        22.75 
TCGA-ZG-A9NI 
        4.34 

$`1Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       60.23        46.55        47.80        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7791 
       38.37        25.87        20.55        14.53        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.31         4.77        28.41        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 
       50.70        49.35        47.15        46.52        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        9.53        25.48        18.84        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       14.37        20.28        11.77        27.12        13.87         5.85 
TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       36.13        29.56        20.94       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       34.85        25.08        29.23         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
        6.71        20.91        38.93        41.19        19.36        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M 
       49.87         4.70         5.82         8.84        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.52        15.81        41.42        25.78        16.31       111.39 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        31.99        31.96        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        71.34        62.79        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        11.67        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        17.98        14.96        11.47        13.48 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.02              0.72 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            79.73            165.17 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           25.680            26.825 
[1] "1.0 - 79.7 (25.7)"  "0.7 - 165.2 (26.8)"
[1] "hr="     "2.7e+07"
D2V2, continuous
                   vv
clus                 T2  T3  T4
  1Q GAIN MUTATED     2  20   3
  1Q GAIN WILD-TYPE 186 261   7
D2V3, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T2               2               186
  T3              20               261
  T4               3                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    17   7
  1Q GAIN WILD-TYPE 321  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17    7
  1Q GAIN WILD-TYPE  321   68
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              17               321
  1               7                68
[1] 2 2
[1] FALSE
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     1  24
  1Q GAIN WILD-TYPE  13 444
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   24
  1Q GAIN WILD-TYPE   13  444
                                        clus
vv                                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 24               444
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    11  13   0   0
  1Q GAIN WILD-TYPE 299 125   5  15
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              11               299
  R1              13               125
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, continuous
D2V8, continuous
D2V9, continuous
D2V10, continuous
D2V11, continuous
D2V12, continuous
D2V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       0                         0     8
  1Q GAIN WILD-TYPE     2                         7   138
D2V14, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   8               138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    10   0
  2P GAIN WILD-TYPE 463   8
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               471 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                0                 8 
$`2P GAIN MUTATED`
TCGA-4L-AA1F TCGA-EJ-A65M TCGA-FC-A4JI TCGA-HC-8256 TCGA-HC-A631 TCGA-KK-A8IF 
       11.51         7.56        13.45        28.27         1.78        26.43 
TCGA-KK-A8IK TCGA-YL-A8S8 TCGA-YL-A8SQ TCGA-ZG-A9LN 
       51.39        62.14        62.79         3.78 

$`2P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       14.83        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8257 
       17.85        24.56        31.43        19.36        22.42        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL 
       15.88         1.15        22.36         0.76         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       11.77        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       67.43        69.27        82.36        66.18       113.98        51.25 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        58.39        79.73         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       51.45        48.72        71.77        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       32.45       114.38        71.34         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.78              0.72 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            62.79            165.17 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            19.94             26.99 
[1] "1.8 - 62.8 (19.9)"  "0.7 - 165.2 (27.0)"
[1] "hr="     "9200000"
D3V2, continuous
                   vv
clus                 T2  T3  T4
  2P GAIN MUTATED     4   6   0
  2P GAIN WILD-TYPE 184 275  10
D3V3, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T2               4               184
  T3               6               275
  T4               0                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     7   1
  2P GAIN WILD-TYPE 331  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      7    1
  2P GAIN WILD-TYPE  331   74
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               7               331
  1               1                74
[1] 2 2
[1] FALSE
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  10
  2P GAIN WILD-TYPE  14 458
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   10
  2P GAIN WILD-TYPE   14  458
                                        clus
vv                                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 10               458
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED     4   5   0   0
  2P GAIN WILD-TYPE 306 133   5  15
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               4               306
  R1               5               133
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, continuous
D3V8, continuous
D3V9, continuous
D3V10, continuous
D3V11, continuous
D3V12, continuous
D3V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0     0
  2P GAIN WILD-TYPE     2                         7   146
D3V14, multiclass

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED     7   0
  2Q GAIN WILD-TYPE 466   8
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7               474 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                0                 8 
$`2Q GAIN MUTATED`
TCGA-4L-AA1F TCGA-EJ-A65M TCGA-FC-A4JI TCGA-HC-A631 TCGA-KK-A8IF TCGA-YL-A8SQ 
       11.51         7.56        13.45         1.78        26.43        62.79 
TCGA-ZG-A9LN 
        3.78 

$`2Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       14.83        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 
        1.58        15.88         1.15        22.36         0.76         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
        2.73        67.43        69.27        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        37.25        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        45.86        46.29        32.45       114.38        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
        4.27        11.67        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       20.28        19.17        12.43        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.78              0.72 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            62.79            165.17 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           11.510            27.055 
[1] "1.8 - 62.8 (11.5)"  "0.7 - 165.2 (27.1)"
[1] "hr="     "3300000"
D4V2, continuous
                   vv
clus                 T2  T3  T4
  2Q GAIN MUTATED     2   5   0
  2Q GAIN WILD-TYPE 186 276  10
D4V3, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T2               2               186
  T3               5               276
  T4               0                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     5   1
  2Q GAIN WILD-TYPE 333  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5    1
  2Q GAIN WILD-TYPE  333   74
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               5               333
  1               1                74
[1] 2 2
[1] FALSE
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0   7
  2Q GAIN WILD-TYPE  14 461
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0    7
  2Q GAIN WILD-TYPE   14  461
                                        clus
vv                                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  7               461
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED     2   4   0   0
  2Q GAIN WILD-TYPE 308 134   5  15
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               2               308
  R1               4               134
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, continuous
D4V8, continuous
D4V9, continuous
D4V10, continuous
D4V11, continuous
D4V12, continuous
D4V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0     0
  2Q GAIN WILD-TYPE     2                         7   146
D4V14, multiclass

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    36   2
  3P GAIN WILD-TYPE 437   6
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               38               443 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                 6 
$`3P GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5771 TCGA-CH-5791 TCGA-EJ-5514 TCGA-EJ-5518 
       35.01         0.92        13.02        33.01        36.23        52.27 
TCGA-EJ-5531 TCGA-EJ-7782 TCGA-EJ-7792 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6499 
       41.85        38.37        17.29        15.42        13.45        50.73 
TCGA-G9-A9S0 TCGA-HC-8216 TCGA-HC-A631 TCGA-HC-A6AS TCGA-HC-A76W TCGA-HI-7168 
       26.01        22.42         1.78         1.45         7.00        78.61 
TCGA-KK-A7B4 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8II TCGA-KK-A8IK 
       20.94        63.48         2.73        26.43       113.98        51.39 
TCGA-VP-A872 TCGA-VP-A87H TCGA-XJ-A83G TCGA-XK-AAIV TCGA-YJ-A8SW TCGA-YL-A8S8 
      111.39        21.80        38.04        37.25         4.87        62.14 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       14.04        53.36        11.67        29.85        20.28        19.17 
TCGA-ZG-A9LS TCGA-ZG-A9LZ 
       16.96        22.75 

$`3P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        31.00         1.02         2.04 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
       24.03         2.04        15.98        26.99         9.99        32.02 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 
       48.53        38.53        60.23        46.55        47.80        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       60.23        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       23.90        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       18.15        19.59         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V 
        4.54         4.31         4.77        28.41        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 
       25.15        27.29        58.22        56.75        64.18        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         4.93         9.53        25.48        18.84 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       13.55        27.12        13.87         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       36.13        29.56        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH 
       31.79        32.91        67.43        69.27        82.36        66.18 
TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 
       15.81        41.42        44.91        25.78        16.31        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       32.19         3.91        37.05        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        31.99        31.96        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 
       52.96        49.02        51.45        48.72        71.77        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
        8.98        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13         4.27        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LU TCGA-ZG-A9LY 
       36.43        22.59        12.43         3.78        19.04        12.16 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.92              0.72 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           113.98            165.17 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            24.38             27.02 
[1] "0.9 - 114.0 (24.4)" "0.7 - 165.2 (27.0)"
[1] "hr=" "4.2"
D5V2, continuous
                   vv
clus                 T2  T3  T4
  3P GAIN MUTATED     7  28   3
  3P GAIN WILD-TYPE 181 253   7
D5V3, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T2               7               181
  T3              28               253
  T4               3                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    26  11
  3P GAIN WILD-TYPE 312  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26   11
  3P GAIN WILD-TYPE  312   64
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              26               312
  1              11                64
[1] 2 2
[1] FALSE
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3  35
  3P GAIN WILD-TYPE  11 433
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   35
  3P GAIN WILD-TYPE   11  433
                                        clus
vv                                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               3                11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 35               433
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    17  17   1   1
  3P GAIN WILD-TYPE 293 121   4  14
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              17               293
  R1              17               121
  R2               1                 4
  RX               1                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"
D5V7, continuous
D5V8, continuous
D5V9, continuous
D5V10, continuous
D5V11, continuous
D5V12, continuous
D5V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         1    11
  3P GAIN WILD-TYPE     2                         6   135
D5V14, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  11               135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    49   3
  3Q GAIN WILD-TYPE 424   5
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               52               429 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                 5 
$`3Q GAIN MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5514 
       11.51        35.01        13.02        26.99        33.01        36.23 
TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7782 TCGA-EJ-7792 
       52.27        51.88        39.75        41.85        38.37        17.29 
TCGA-EJ-A65J TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6363 TCGA-G9-6499 
       14.83        15.42        13.45        66.67        45.30        50.73 
TCGA-G9-A9S0 TCGA-HC-8216 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AS TCGA-HC-A76W 
       26.01        22.42         0.76         1.78         1.45         7.00 
TCGA-HC-A8CY TCGA-HI-7168 TCGA-J4-AATZ TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IA 
        9.53        78.61        13.55        29.56        20.94        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8II TCGA-KK-A8IK TCGA-VN-A88R 
        2.73        67.43        26.43       113.98        51.39        25.78 
TCGA-VP-A872 TCGA-VP-A87H TCGA-XJ-A83G TCGA-XK-AAIV TCGA-YJ-A8SW TCGA-YL-A8S8 
      111.39        21.80        38.04        37.25         4.87        62.14 
TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A9L0 TCGA-ZG-A9L5 
       71.34        14.04        53.36        60.99        11.67        29.85 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LZ TCGA-ZG-A9MC 
       20.28        19.17        22.75        14.96 

$`3Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 
       24.03         2.04        15.98         9.99        32.02         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5522 
       38.53        60.23        46.55        47.80        64.50        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 
       43.07        36.66        38.76        60.23        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 
       27.68         6.28        24.39        23.90        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7793 
       20.55        14.53        14.14        18.15        19.59         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       81.04        67.99        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 
       25.15        27.29        58.22        56.75        64.18        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 
       22.32         1.58        15.88         1.15        22.36         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         3.48         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 
        4.41         4.93        25.48        18.84        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        14.37        20.28        11.77        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        5.85        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        32.84        34.95        36.13        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8ID TCGA-KK-A8IG 
       21.96        65.82        31.79        32.91        69.27        82.36 
TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       66.18        51.25        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A875 
       15.52        15.81        41.42        44.91        16.31        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       32.19         3.91        37.05        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        31.99        31.96        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 
       52.96        49.02        51.45        48.72        71.77        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        46.29        32.45       114.38        62.79         8.98 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
       13.28        10.13         4.27        37.94        36.43        22.59 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 
       12.43         3.78        16.96        19.04        12.16        17.98 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.76              0.72 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           113.98            165.17 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            26.71             26.66 
[1] "0.8 - 114.0 (26.7)" "0.7 - 165.2 (26.7)"
[1] "hr=" "5.3"
D6V2, continuous
                   vv
clus                 T2  T3  T4
  3Q GAIN MUTATED     8  40   4
  3Q GAIN WILD-TYPE 180 241   6
D6V3, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T2               8               180
  T3              40               241
  T4               4                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    36  14
  3Q GAIN WILD-TYPE 302  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     36   14
  3Q GAIN WILD-TYPE  302   61
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              36               302
  1              14                61
[1] 2 2
[1] FALSE
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3  49
  3Q GAIN WILD-TYPE  11 419
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   49
  3Q GAIN WILD-TYPE   11  419
                                        clus
vv                                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               3                11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 49               419
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    24  24   1   1
  3Q GAIN WILD-TYPE 286 114   4  14
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              24               286
  R1              24               114
  R2               1                 4
  RX               1                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"
D6V7, continuous
D6V8, continuous
D6V9, continuous
D6V10, continuous
D6V11, continuous
D6V12, continuous
D6V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         1    15
  3Q GAIN WILD-TYPE     2                         6   131
D6V14, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  15               131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     8   0
  4P GAIN WILD-TYPE 465   8
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               473 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                 8 
$`4P GAIN MUTATED`
TCGA-EJ-5542 TCGA-G9-6499 TCGA-HC-7080 TCGA-KK-A8I4 TCGA-VP-A875 TCGA-YL-A8HO 
       29.06        50.73        36.36        67.99        75.91        71.77 
TCGA-YL-A8SR TCGA-ZG-A9LY 
        8.98        12.16 

$`4P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       60.23        41.85        47.87        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        5.85        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       30.38        15.58        22.55         6.64        58.39        79.73 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
        6.71        20.91        38.93        41.19        19.36        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87         4.70         5.82         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       16.31       111.39       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        37.25        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        51.45        48.72        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       28.34         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LZ 
       19.17        12.43         3.78        16.96        19.04        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             8.98              0.72 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            75.91            165.17 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           43.545            26.300 
[1] "9.0 - 75.9 (43.5)"  "0.7 - 165.2 (26.3)"
[1] "hr="     "2.6e+07"
D7V2, continuous
                   vv
clus                 T2  T3  T4
  4P GAIN MUTATED     1   7   0
  4P GAIN WILD-TYPE 187 274  10
D7V3, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T2               1               187
  T3               7               274
  T4               0                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6   2
  4P GAIN WILD-TYPE 332  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    2
  4P GAIN WILD-TYPE  332   73
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               6               332
  1               2                73
[1] 2 2
[1] FALSE
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   8
  4P GAIN WILD-TYPE  14 460
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    8
  4P GAIN WILD-TYPE   14  460
                                        clus
vv                                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  8               460
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     5   3   0   0
  4P GAIN WILD-TYPE 305 135   5  15
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               5               305
  R1               3               135
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, continuous
D7V8, continuous
D7V9, continuous
D7V10, continuous
D7V11, continuous
D7V12, continuous
D7V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         0     3
  4P GAIN WILD-TYPE     2                         7   143
D7V14, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    10   0
  4Q GAIN WILD-TYPE 463   8
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               471 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                 8 
$`4Q GAIN MUTATED`
TCGA-EJ-5542 TCGA-HC-7080 TCGA-KK-A8I4 TCGA-V1-A8WV TCGA-VP-A875 TCGA-XK-AAJT 
       29.06        36.36        67.99        22.55        75.91        47.15 
TCGA-YJ-A8SW TCGA-YL-A8HO TCGA-ZG-A9LS TCGA-ZG-A9LY 
        4.87        71.77        16.96        12.16 

$`4Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       60.23        41.85        47.87        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.93        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       13.87         5.85        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       20.94       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       52.08        30.38        15.58         6.64        58.39        79.73 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
        6.71        20.91        38.93        41.19        19.36        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87         4.70         5.82         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       16.31       111.39       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        37.25        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       36.95        51.81        32.19        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       51.45        48.72        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       37.94        36.43        29.85        22.59        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       12.43         3.78        19.04        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             4.87              0.72 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            75.91            165.17 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            32.71             26.43 
[1] "4.9 - 75.9 (32.7)"  "0.7 - 165.2 (26.4)"
[1] "hr="     "2.6e+07"
D8V2, continuous
                   vv
clus                 T2  T3  T4
  4Q GAIN MUTATED     1   9   0
  4Q GAIN WILD-TYPE 187 272  10
D8V3, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T2               1               187
  T3               9               272
  T4               0                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     6   4
  4Q GAIN WILD-TYPE 332  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      6    4
  4Q GAIN WILD-TYPE  332   71
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               6               332
  1               4                71
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   9
  4Q GAIN WILD-TYPE  13 459
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    9
  4Q GAIN WILD-TYPE   13  459
                                        clus
vv                                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  9               459
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     5   5   0   0
  4Q GAIN WILD-TYPE 305 133   5  15
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               5               305
  R1               5               133
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, continuous
D8V8, continuous
D8V9, continuous
D8V10, continuous
D8V11, continuous
D8V12, continuous
D8V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         0     2
  4Q GAIN WILD-TYPE     2                         7   144
D8V14, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               153 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-7115 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797        TCGA-FC-7708 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332        TCGA-G9-6333 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7081 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7750 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HI-7171 
"4Q GAIN WILD-TYPE" 

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    23   0
  5P GAIN WILD-TYPE 450   8
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23               458 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                0                 8 
$`5P GAIN MUTATED`
TCGA-CH-5761 TCGA-EJ-5495 TCGA-FC-A4JI TCGA-HC-A4ZV TCGA-J9-A52E TCGA-KK-A7B4 
        0.92        33.11        13.45         0.76        10.62        20.94 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IK TCGA-V1-A9O5 TCGA-VP-A872 
       63.48         2.73        26.43        51.39        58.39       111.39 
TCGA-VP-A875 TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8SL TCGA-YL-A9WH 
       75.91        21.80        37.25        71.77        32.45        14.04 
TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LU 
       10.13        11.67        29.85        19.17        19.04 

$`5P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 
        1.58        15.88         1.15        22.36         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG 
       65.82        31.79        32.91        67.43        69.27        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18       113.98        51.25        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 
       30.38        15.58        22.55         6.64        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        31.99        31.96        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        53.06        45.86        46.29       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       62.79         8.98        53.36        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9KY 
       49.91        28.34         3.09        14.53        13.28         4.27 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN 
       37.94        36.43        22.59        20.28        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       16.96        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.76              0.72 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           111.39            165.17 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           21.800            27.005 
[1] "0.8 - 111.4 (21.8)" "0.7 - 165.2 (27.0)"
[1] "hr="     "2.6e+07"
D9V2, continuous
                   vv
clus                 T2  T3  T4
  5P GAIN MUTATED     1  20   2
  5P GAIN WILD-TYPE 187 261   8
D9V3, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T2               1               187
  T3              20               261
  T4               2                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    12  10
  5P GAIN WILD-TYPE 326  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     12   10
  5P GAIN WILD-TYPE  326   65
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              12               326
  1              10                65
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  22
  5P GAIN WILD-TYPE  13 446
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   22
  5P GAIN WILD-TYPE   13  446
                                        clus
vv                                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 22               446
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED     9  12   1   1
  5P GAIN WILD-TYPE 301 126   4  14
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0               9               301
  R1              12               126
  R2               1                 4
  RX               1                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"
D9V7, continuous
D9V8, continuous
D9V9, continuous
D9V10, continuous
D9V11, continuous
D9V12, continuous
D9V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       0                         0     2
  5P GAIN WILD-TYPE     2                         7   144
D9V14, multiclass
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2               153 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5762        TCGA-CH-5763 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5496 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7794        TCGA-EJ-7797        TCGA-FC-7708        TCGA-FC-7961 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6329        TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075        TCGA-HC-7077 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7081 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7750 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HI-7171 
"5P GAIN WILD-TYPE" 

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    12   0
  5Q GAIN WILD-TYPE 461   8
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               469 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                 8 
$`5Q GAIN MUTATED`
TCGA-EJ-5495 TCGA-J9-A52E TCGA-J9-A8CL TCGA-KK-A7B4 TCGA-KK-A8IA TCGA-KK-A8IB 
       33.11        10.62        13.32        20.94        63.48         2.73 
TCGA-VP-A875 TCGA-VP-A87H TCGA-YL-A8HO TCGA-YL-A8SL TCGA-ZG-A8QZ TCGA-ZG-A9L0 
       75.91        21.80        71.77        32.45        10.13        11.67 

$`5Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       27.16        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
       27.12        13.87         5.85        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 
       49.94        32.84        34.95        36.13        29.56        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC 
      101.79        21.96        65.82        31.79        32.91        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       48.72        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO 
       45.14        28.77        53.06        45.86        46.29       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       13.28         4.27        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2.73              0.72 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            75.91            165.17 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            21.37             26.99 
[1] "2.7 - 75.9 (21.4)"  "0.7 - 165.2 (27.0)"
[1] "hr="     "9400000"
D10V2, continuous
                   vv
clus                 T2  T3  T4
  5Q GAIN MUTATED     0  12   0
  5Q GAIN WILD-TYPE 188 269  10
D10V3, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T2               0               188
  T3              12               269
  T4               0                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     5   6
  5Q GAIN WILD-TYPE 333  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5    6
  5Q GAIN WILD-TYPE  333   69
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               5               333
  1               6                69
[1] 2 2
[1] FALSE
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  12
  5Q GAIN WILD-TYPE  14 456
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   12
  5Q GAIN WILD-TYPE   14  456
                                        clus
vv                                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 12               456
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED     4   6   1   1
  5Q GAIN WILD-TYPE 306 132   4  14
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0               4               306
  R1               6               132
  R2               1                 4
  RX               1                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"
D10V7, continuous
D10V8, continuous
D10V9, continuous
D10V10, continuous
D10V11, continuous
D10V12, continuous
D10V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         0     1
  5Q GAIN WILD-TYPE     2                         7   145
D10V14, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797        TCGA-FC-7708 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332        TCGA-G9-6333 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     8   1
  6P GAIN WILD-TYPE 465   7
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                9               472 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                 7 
$`6P GAIN MUTATED`
TCGA-HI-7168 TCGA-KC-A7FA TCGA-KK-A59Z TCGA-V1-A8WV TCGA-XJ-A9DX TCGA-XK-AAJT 
       78.61        19.66        86.40        22.55        31.99        47.15 
TCGA-YL-A9WJ TCGA-ZG-A9LS TCGA-ZG-A9NI 
       60.99        16.96         4.34 

$`6P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        7.00         4.93         9.53        25.48        18.84        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       43.66        21.86         8.65         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       56.28        44.68       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       52.08        30.38        15.58         6.64        58.39        79.73 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
        6.71        20.91        38.93        41.19        19.36        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87         4.70         5.82         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       16.31       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        37.25        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       36.95        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
        8.98        14.04        53.36        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       28.34         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       19.17        12.43         3.78        19.04        12.16        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       17.98        14.96        11.47        13.48 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             4.34              0.72 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            86.40            165.17 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           31.990            26.545 
[1] "4.3 - 86.4 (32.0)"  "0.7 - 165.2 (26.5)"
[1] "hr=" "7.1"
D11V2, continuous
                   vv
clus                 T2  T3  T4
  6P GAIN MUTATED     1   8   0
  6P GAIN WILD-TYPE 187 273  10
D11V3, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T2               1               187
  T3               8               273
  T4               0                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5   4
  6P GAIN WILD-TYPE 333  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    4
  6P GAIN WILD-TYPE  333   71
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               5               333
  1               4                71
[1] 2 2
[1] FALSE
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0   9
  6P GAIN WILD-TYPE  14 459
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    9
  6P GAIN WILD-TYPE   14  459
                                        clus
vv                                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  9               459
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED     4   5   0   0
  6P GAIN WILD-TYPE 306 133   5  15
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               4               306
  R1               5               133
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, continuous
D11V8, continuous
D11V9, continuous
D11V10, continuous
D11V11, continuous
D11V12, continuous
D11V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       0                         0     1
  6P GAIN WILD-TYPE     2                         7   145
D11V14, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7169 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     5   0
  6Q GAIN WILD-TYPE 468   8
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5               476 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 8 
$`6Q GAIN MUTATED`
TCGA-HI-7168 TCGA-KK-A59Z TCGA-XJ-A9DX TCGA-XK-AAJT TCGA-ZG-A9LS 
       78.61        86.40        31.99        47.15        16.96 

$`6Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        7.00         4.93         9.53        25.48        18.84        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        56.28        44.68       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       30.58        41.39        36.95        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            16.96              0.72 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            86.40            165.17 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           47.150            26.365 
[1] "17.0 - 86.4 (47.1)" "0.7 - 165.2 (26.4)"
[1] "hr="     "9200000"
D12V2, continuous
                   vv
clus                 T2  T3  T4
  6Q GAIN MUTATED     1   4   0
  6Q GAIN WILD-TYPE 187 277  10
D12V3, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T2               1               187
  T3               4               277
  T4               0                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3   2
  6Q GAIN WILD-TYPE 335  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    2
  6Q GAIN WILD-TYPE  335   73
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               3               335
  1               2                73
[1] 2 2
[1] FALSE
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0   5
  6Q GAIN WILD-TYPE  14 463
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    5
  6Q GAIN WILD-TYPE   14  463
                                        clus
vv                                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  5               463
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED     2   3   0   0
  6Q GAIN WILD-TYPE 308 135   5  15
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0               2               308
  R1               3               135
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, continuous
D12V8, continuous
D12V9, continuous
D12V10, continuous
D12V11, continuous
D12V12, continuous
D12V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         0     1
  6Q GAIN WILD-TYPE     2                         7   145
D12V14, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7169 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    99   0
  7P GAIN WILD-TYPE 374   8
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               99               382 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 8 
$`7P GAIN MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 
       11.51        35.01         2.04        24.03        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5509 TCGA-EJ-5525 
       26.99        33.01        27.16        33.11        48.13        36.66 
TCGA-EJ-5542 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-7786 
       29.06        93.70        37.81         6.28        25.68        14.53 
TCGA-EJ-7789 TCGA-EJ-A46F TCGA-EJ-A65M TCGA-EJ-A7NH TCGA-EJ-A8FN TCGA-EJ-AB20 
       18.15        25.74         7.56        15.58        10.82         4.31 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6366 TCGA-G9-6371 TCGA-G9-6377 
       15.42        13.45        66.67         3.32        40.31        31.50 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7523 TCGA-HC-7742 TCGA-HC-8260 
       56.75        64.18        50.73        28.18         1.48        22.55 
TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AP TCGA-HC-A76W 
       17.95        15.88         0.76         1.78         2.33         7.00 
TCGA-HI-7168 TCGA-J4-8198 TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN TCGA-KK-A59Z 
       78.61        20.19        10.62        13.32        40.67        86.40 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B4 TCGA-KK-A8I4 
       58.19         6.44        51.68        32.84        20.94        67.99 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IK TCGA-M7-A721 
       63.48         2.73        26.43        82.36        51.39        13.15 
TCGA-QU-A6IM TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A9O7 
       41.00        13.32        28.18        52.08        22.55        79.73 
TCGA-V1-A9OX TCGA-V1-A9Z7 TCGA-V1-A9ZI TCGA-VN-A88P TCGA-VP-A872 TCGA-VP-A875 
        8.42         4.27         4.70        41.42       111.39        75.91 
TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83H TCGA-XK-AAIV 
       85.18        21.80        44.88        45.47        42.08        37.25 
TCGA-XK-AAJ3 TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SB 
       41.49         4.87        48.72        71.77        62.14        56.52 
TCGA-YL-A8SF TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       45.14       114.38        62.79         8.98        14.04        53.36 
TCGA-YL-A9WK TCGA-ZG-A8QX TCGA-ZG-A9L0 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LZ 
       62.37        14.53        11.67        19.17        12.43        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       17.98        11.47         4.34 

$`7P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5762 
        1.02        13.02        31.00         1.02         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 
       12.00         1.02        23.01         1.02        15.06         2.04 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5496 TCGA-EJ-5497 
        9.99        32.02         2.99        29.00        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 
       30.31        27.19        23.90        38.93        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 
       64.50        51.88        68.35        43.07        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7218 
       60.23        41.85        47.87        88.34        74.10        83.57 
TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       36.13        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35        27.68        24.39        23.90        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       20.55        14.14        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       21.60        20.58        17.23        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61        28.70         8.22        14.20         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB27 
        4.21         9.27         9.83         8.75         4.54         4.77 
TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.41        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       87.35        81.04        67.99        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 
       46.52        47.44        45.30        39.39        44.81        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       39.95        38.01        26.66        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       27.29        58.22        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       35.34        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
       23.57         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 
        2.27        22.32         1.58         1.15        22.36         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        4.41         4.93         9.53        25.48        18.84        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       82.92        43.69        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.87         5.85        15.22        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY 
        8.88        11.57       113.10        56.28        44.68       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
      113.33        67.07        52.93        58.36        27.02        34.65 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I6 
       49.94        34.95        36.13        29.56       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH 
       65.82        31.79        32.91        67.43        69.27        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
      113.98        51.25        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       12.62        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
        3.19       140.19       122.17        86.14        18.12        11.90 
TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       41.23        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA 
       30.38        15.58         6.64        58.39         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OY 
       38.93        41.19        19.36        12.20        15.65         5.59 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
        6.15        17.75        49.87         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R 
       24.53         6.21        15.52        15.81        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D 
       16.31       109.58        97.41        23.93        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR 
       66.97        53.36        42.94        14.76        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       37.05        38.04        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        40.04        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       51.81        32.19        25.48        52.96        49.02        51.45 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       60.56        16.83        41.46        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
       46.29        32.45        71.34        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 
       28.34         3.09        13.28        10.13         4.27        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9LS 
       36.43        29.85        22.59        20.28         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND 
       19.04        12.16        14.96        13.48 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.76              0.72 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           114.38            165.17 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            26.43             26.84 
[1] "0.8 - 114.4 (26.4)" "0.7 - 165.2 (26.8)"
[1] "hr="     "2.7e+08"
D13V2, continuous
                   vv
clus                 T2  T3  T4
  7P GAIN MUTATED    29  69   1
  7P GAIN WILD-TYPE 159 212   9
D13V3, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T2              29               159
  T3              69               212
  T4               1                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    69  17
  7P GAIN WILD-TYPE 269  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     69   17
  7P GAIN WILD-TYPE  269   58
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              69               269
  1              17                58
[1] 2 2
[1] FALSE
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     2  97
  7P GAIN WILD-TYPE  12 371
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   97
  7P GAIN WILD-TYPE   12  371
                                        clus
vv                                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               2                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 97               371
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED    49  42   1   4
  7P GAIN WILD-TYPE 261  96   4  11
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              49               261
  R1              42                96
  R2               1                 4
  RX               4                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"
D13V7, continuous
D13V8, continuous
D13V9, continuous
D13V10, continuous
D13V11, continuous
D13V12, continuous
D13V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       0                         1    26
  7P GAIN WILD-TYPE     2                         6   120
D13V14, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  26               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    92   0
  7Q GAIN WILD-TYPE 381   8
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               92               389 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 8 
$`7Q GAIN MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5791 
       11.51        35.01        24.03        13.02        15.98        33.01 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5509 TCGA-EJ-5525 TCGA-EJ-5542 TCGA-EJ-7125 
       27.16        33.11        48.13        36.66        29.06        93.70 
TCGA-EJ-7314 TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-A46F TCGA-EJ-A65M 
       37.81         6.28        25.68        18.15        25.74         7.56 
TCGA-EJ-A7NH TCGA-EJ-A8FN TCGA-EJ-AB20 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 
       15.58        10.82         4.31        15.42        13.45        66.67 
TCGA-G9-6366 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
        3.32        40.31        31.50        56.75        64.18        50.73 
TCGA-G9-7523 TCGA-HC-7742 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-A4ZV 
       28.18         1.48        22.55        17.95        15.88         0.76 
TCGA-HC-A631 TCGA-HC-A6AP TCGA-HC-A76W TCGA-HI-7168 TCGA-J4-8198 TCGA-J9-A52E 
        1.78         2.33         7.00        78.61        20.19        10.62 
TCGA-J9-A8CL TCGA-J9-A8CN TCGA-KK-A59Z TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AY 
       13.32        40.67        86.40        58.19         6.44        51.68 
TCGA-KK-A7B0 TCGA-KK-A7B4 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IG 
       32.84        20.94        63.48         2.73        26.43        82.36 
TCGA-KK-A8IK TCGA-M7-A721 TCGA-QU-A6IM TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8WL 
       51.39        13.15        41.00        13.32        28.18        52.08 
TCGA-V1-A8WV TCGA-V1-A9O7 TCGA-V1-A9OX TCGA-V1-A9Z7 TCGA-V1-A9ZI TCGA-VN-A88P 
       22.55        79.73         8.42         4.27         4.70        41.42 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ 
      111.39        75.91        85.18        21.80        44.88        45.47 
TCGA-XJ-A83H TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SB 
       42.08         4.87        48.72        71.77        62.14        56.52 
TCGA-YL-A8SF TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WK 
       45.14       114.38        62.79         8.98        14.04        62.37 
TCGA-ZG-A8QX TCGA-ZG-A9L0 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       14.53        11.67        19.17        12.43        22.75        17.98 
TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       11.47         4.34 

$`7Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 
        2.04        26.99         9.99        32.02         2.99        29.00 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       38.76        39.75        60.23        41.85        47.87        88.34 
TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       74.10        83.57        36.13        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 
       27.09        35.18        30.35        27.68        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 
       38.37        25.87        20.55        14.53        14.14        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       18.41        21.90        14.83        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FO TCGA-EJ-A8FP 
       14.20         6.48        15.65         4.21         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V 
        8.75         4.54         4.77        28.41        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6373 
       39.39        44.81        40.18        39.95        38.01        26.66 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 
       37.97        58.45        25.15        27.29        58.22        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 
       38.96        27.91        30.97        35.34        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 
        0.72         2.10        31.69        23.57         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8262 TCGA-HC-8264 
       28.27        23.87         2.17         2.27        22.32         1.58 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        1.15        22.36         2.01         2.20         1.61        17.42 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        3.48         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 
       25.48        18.84        88.24        82.92        43.69        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CM 
       11.77        13.55        27.12        13.87         5.85        15.22 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       56.28        44.68       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AQ 
       67.59       115.13        49.25       113.33        67.07        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       58.36        27.02        34.65        49.94        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       29.56        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       32.91        67.43        69.27        66.18       113.98        51.25 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 
       20.65        47.28         5.19        21.14        12.62        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MJ 
      122.17        86.14        18.12        11.90        41.23        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WS 
       16.70        14.73        39.29        53.16        30.38        15.58 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        58.39         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       19.36        12.20        15.65         5.59         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       49.87         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 
       15.52        15.81        44.91        25.78        16.31       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       97.41        23.93        55.56        60.92        66.97        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       42.94        14.76        32.19         3.91        37.05        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       51.81        32.19        25.48        52.96        49.02        51.45 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       60.56        16.83        41.46        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL 
       46.29        32.45        71.34        53.36        60.99        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       49.91        28.34         3.09        13.28        10.13         4.27 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LN 
       37.94        36.43        29.85        22.59        20.28         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND 
       16.96        19.04        12.16        14.96        13.48 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.76              0.72 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           114.38            165.17 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            25.71             27.02 
[1] "0.8 - 114.4 (25.7)" "0.7 - 165.2 (27.0)"
[1] "hr="     "9.7e+07"
D14V2, continuous
                   vv
clus                 T2  T3  T4
  7Q GAIN MUTATED    28  63   1
  7Q GAIN WILD-TYPE 160 218   9
D14V3, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T2              28               160
  T3              63               218
  T4               1                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    67  12
  7Q GAIN WILD-TYPE 271  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     67   12
  7Q GAIN WILD-TYPE  271   63
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              67               271
  1              12                63
[1] 2 2
[1] FALSE
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2  90
  7Q GAIN WILD-TYPE  12 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2   90
  7Q GAIN WILD-TYPE   12  378
                                        clus
vv                                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               2                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 90               378
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED    44  40   1   4
  7Q GAIN WILD-TYPE 266  98   4  11
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              44               266
  R1              40                98
  R2               1                 4
  RX               4                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"
D14V7, continuous
D14V8, continuous
D14V9, continuous
D14V10, continuous
D14V11, continuous
D14V12, continuous
D14V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       0                         1    23
  7Q GAIN WILD-TYPE     2                         6   123
D14V14, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  23               123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    69   1
  8P GAIN WILD-TYPE 404   7
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               70               411 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                 7 
$`8P GAIN MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-5504 TCGA-EJ-5509 TCGA-EJ-5514 
       11.51        35.01         0.92        28.93        48.13        36.23 
TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7312 
       51.88        36.66        38.76        74.10        93.70        36.13 
TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A7NH TCGA-EJ-AB27 
       25.68        18.15        14.83         7.56        15.58         4.77 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 TCGA-HC-7078 
       15.42        13.45        50.73        38.96        30.97        65.26 
TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A6AO 
        1.48        23.70        15.88         1.15         0.76        17.42 
TCGA-HC-A8CY TCGA-J9-A52B TCGA-J9-A8CM TCGA-KK-A59V TCGA-KK-A59Z TCGA-KK-A6DY 
        9.53        13.87        15.22       113.10        86.40       115.86 
TCGA-KK-A6E8 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IB TCGA-KK-A8IK TCGA-M7-A724 
       58.19        65.82        31.79         2.73        51.39        29.23 
TCGA-QU-A6IL TCGA-V1-A8MF TCGA-V1-A8MM TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9Z7 
        3.19        41.23        39.29        22.55        58.39         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9ZI TCGA-VN-A88M TCGA-VN-A943 TCGA-VP-A87H TCGA-VP-AA1N 
        6.15         4.70         6.21        16.31        21.80        44.88 
TCGA-XK-AAJT TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SK 
       47.15        48.72        71.77        62.14        60.56        46.29 
TCGA-YL-A8SQ TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB 
       62.79        60.99        62.37        29.85        22.59        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9N3 
       12.43        19.04        22.75        11.47 

$`8P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 
        1.02        13.02        31.00         1.02         2.04        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 
       30.31        27.19        23.90        38.93        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       38.53        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       68.35        43.07        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       29.06        88.34        83.57        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        23.90        38.37        25.87        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       14.14        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A6RA 
       23.34        12.92        13.71        18.41        21.90        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
       28.70         8.22        14.20         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.41        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       56.75        64.18        52.93        27.91        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       19.76         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
       44.55         0.72         2.10        31.69        23.57         1.68 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
       22.32         1.58        22.36         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        7.00         4.93        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP 
       27.12         5.85        10.62        13.32        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
        8.65        19.66         8.88        11.57        56.28        44.68 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        67.07         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I9 
       29.56        20.94        67.99       101.79        21.96        32.91 
TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
       63.48        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
      113.98        51.25        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 TCGA-MG-AAMC 
       12.62        13.15        34.85        25.08        18.84         5.69 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU 
       13.32        28.18        40.44        16.70        14.73        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 
       52.08        30.38        15.58         6.64        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I 
        8.42         5.59        17.75        49.87         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       25.51        24.53        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       85.18        55.56        60.92        66.97        53.36        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       37.25        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       51.45        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR 
       53.06        45.86        32.45       114.38        71.34         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       14.04        53.36        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9M4 
       36.43        20.28         3.78        16.96        12.16        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        13.48         4.34 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.76              0.72 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           115.86            165.17 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            29.08             26.43 
[1] "0.8 - 115.9 (29.1)" "0.7 - 165.2 (26.4)"
[1] "hr=" "1.4"
D15V2, continuous
                   vv
clus                 T2  T3  T4
  8P GAIN MUTATED    17  50   3
  8P GAIN WILD-TYPE 171 231   7
D15V3, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T2              17               171
  T3              50               231
  T4               3                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    55  13
  8P GAIN WILD-TYPE 283  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     55   13
  8P GAIN WILD-TYPE  283   62
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              55               283
  1              13                62
[1] 2 2
[1] FALSE
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0  70
  8P GAIN WILD-TYPE  14 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   70
  8P GAIN WILD-TYPE   14  398
                                        clus
vv                                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 70               398
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    34  32   1   1
  8P GAIN WILD-TYPE 276 106   4  14
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              34               276
  R1              32               106
  R2               1                 4
  RX               1                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"
D15V7, continuous
D15V8, continuous
D15V9, continuous
D15V10, continuous
D15V11, continuous
D15V12, continuous
D15V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         1    16
  8P GAIN WILD-TYPE     2                         6   130
D15V14, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  16               130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   120   1
  8Q GAIN WILD-TYPE 353   7
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              121               360 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 7 
$`8Q GAIN MUTATED`
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5761 
       22.06        33.96         3.68        11.51        35.01         0.92 
TCGA-CH-5771 TCGA-EJ-5504 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 
       13.02        28.93        48.13        48.53        36.23        47.80 
TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5532 TCGA-EJ-7123 TCGA-EJ-7125 
       51.88        36.66        38.76        47.87        74.10        93.70 
TCGA-EJ-7312 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-8469 TCGA-EJ-A46F 
       36.13        23.90        25.68        18.15        76.41        25.74 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A7NH TCGA-EJ-AB27 TCGA-FC-7961 
       21.96        14.83         7.56        15.58         4.77        15.42 
TCGA-FC-A4JI TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6499 TCGA-G9-7510 
       13.45         3.32        26.66        31.50        50.73        38.96 
TCGA-G9-7521 TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7742 
       30.97        23.93        65.26        28.60        40.08         1.48 
TCGA-HC-7745 TCGA-HC-8216 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A632 
       23.70        22.42        15.88         1.15         0.76         2.01 
TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A8CY TCGA-J4-A67M TCGA-J9-A52B TCGA-J9-A8CL 
        2.20        17.42         9.53        30.94        13.87        13.32 
TCGA-J9-A8CM TCGA-KC-A4BV TCGA-KK-A59V TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E8 
       15.22        43.66       113.10        86.40       115.86        58.19 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B4 TCGA-KK-A8I4 
       58.36        27.02        34.65        49.94        20.94        67.99 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IG 
       65.82        31.79        32.91        63.48         2.73        82.36 
TCGA-KK-A8IK TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IO TCGA-V1-A8MF 
       51.39        29.23        18.84         3.19       122.17        41.23 
TCGA-V1-A8MG TCGA-V1-A8MM TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9OA 
       28.18        39.29        22.55        58.39        79.73        20.91 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9ZI TCGA-VN-A88M 
       41.19        19.36         4.27         6.15         4.70         6.21 
TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A87H TCGA-VP-AA1N TCGA-XJ-A83G 
       41.42        16.31        75.91        21.80        44.88        38.04 
TCGA-XJ-A83H TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO 
       42.08        37.25        47.15         4.87        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SK TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ 
       62.14        60.56        46.29        62.79         8.98        60.99 
TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       62.37        28.34        11.67        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9N3 
       19.17        12.43        19.04        12.16        22.75        11.47 
TCGA-ZG-A9NI 
        4.34 

$`8Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       20.42        43.79        32.71        25.35        31.96        30.31 
TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       20.22         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 
       13.97         1.97        24.03         1.02        13.02        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         2.04        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 
        1.02        15.06        24.03         2.04        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       26.30        45.73        30.31        27.19        23.90        38.93 
TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5519 
       36.69        38.53        60.23        46.55        52.27        64.50 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5542 
       68.35        43.07        39.75        60.23        41.85        29.06 
TCGA-EJ-7115 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       88.34        83.57        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 
       38.37        25.87        20.55        14.53        14.14        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 
       17.29         3.75        23.05        19.92        77.16        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H 
       24.85        25.18        21.60        20.58        17.23        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61        28.70         8.22        14.20         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        4.31        28.41        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 
       44.81        40.18        39.95        38.01        40.31        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-7509 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       52.93        27.91        35.34        28.18        32.68        26.01 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 
        6.08        30.94         3.68        19.76         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7230 TCGA-HC-7231 
       37.35        14.47        28.54         0.79         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        1.68        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6AN TCGA-HC-A6AP 
       22.32         1.58        22.36         1.78         1.61         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O 
       20.19        12.30        33.01        25.32        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E 
       20.28        11.77        13.55        27.12         5.85        10.62 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X 
       21.86         8.65        19.66         8.88        11.57        56.28 
TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       44.68        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AY 
       49.25       113.33        67.07         6.44        52.93        51.68 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I6 
       32.84        34.95        36.13        29.56       101.79        21.96 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       67.43        69.27        26.43        66.18       113.98        51.25 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-MG-AAMC TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP 
       34.85        25.08         5.69        41.00       140.19        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        11.90        13.32        40.44        16.70        14.73 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O9 
       53.16        52.08        30.38        15.58         6.64         6.71 
TCGA-V1-A9OF TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z9 
       38.93        12.20        15.65         8.42         5.59        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N 
       49.87         5.82         8.84        25.51        24.53        15.52 
TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 
       15.81        44.91        25.78       111.39       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       23.93        85.18        55.56        60.92        66.97        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        31.99        31.96        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 
       41.49        30.58        41.39        36.95        51.81        32.19 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SB 
       25.48        52.96        49.02        51.45        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL 
       41.46        45.14        28.77        53.06        45.86        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WL TCGA-YL-A9WX 
      114.38        71.34        14.04        53.36        24.33        49.91 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13         4.27        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND 
       36.43         3.78        16.96        17.98        14.96        13.48 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.76              0.72 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           122.17            165.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            28.60             25.94 
[1] "0.8 - 122.2 (28.6)" "0.7 - 165.2 (25.9)"
[1] "hr=" "3"  
D16V2, continuous
                   vv
clus                 T2  T3  T4
  8Q GAIN MUTATED    29  89   3
  8Q GAIN WILD-TYPE 159 192   7
D16V3, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T2              29               159
  T3              89               192
  T4               3                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    88  25
  8Q GAIN WILD-TYPE 250  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     88   25
  8Q GAIN WILD-TYPE  250   50
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              88               250
  1              25                50
[1] 2 2
[1] FALSE
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     2 119
  8Q GAIN WILD-TYPE  12 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2  119
  8Q GAIN WILD-TYPE   12  349
                                        clus
vv                                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               2                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                119               349
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED    62  49   1   5
  8Q GAIN WILD-TYPE 248  89   4  10
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              62               248
  R1              49                89
  R2               1                 4
  RX               5                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"
D16V7, continuous
D16V8, continuous
D16V9, continuous
D16V10, continuous
D16V11, continuous
D16V12, continuous
D16V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       0                         2    25
  8Q GAIN WILD-TYPE     2                         5   121
D16V14, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  25               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    31   0
  9P GAIN WILD-TYPE 442   8
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               31               450 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 8 
$`9P GAIN MUTATED`
TCGA-CH-5771 TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5514 TCGA-EJ-5526 TCGA-EJ-7789 
       13.02        33.01        33.11        36.23        38.76        18.15 
TCGA-EJ-A65F TCGA-FC-A4JI TCGA-HC-7821 TCGA-HC-8266 TCGA-HC-A8CY TCGA-J4-AATZ 
       18.41        13.45        31.43         1.15         9.53        13.55 
TCGA-KK-A8I4 TCGA-V1-A8MJ TCGA-V1-A8WV TCGA-V1-A9OL TCGA-VP-A872 TCGA-VP-A875 
       67.99        40.44        22.55        19.36       111.39        75.91 
TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8SC TCGA-YL-A8SL TCGA-YL-A8SQ 
       21.80        37.25        71.77        41.46        32.45        62.79 
TCGA-YL-A9WK TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LS TCGA-ZG-A9M4 
       62.37        11.67        29.85        19.17        16.96        17.98 
TCGA-ZG-A9NI 
        4.34 

$`9P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 
        1.02        15.06        24.03         2.04        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 
        9.99        32.02         2.99        29.00        27.16        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        48.53        38.53        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        14.53        14.14        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G 
       23.80        21.96        23.34        12.92        13.71        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       15.42        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        17.85        24.56        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
        1.58        15.88        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         7.00         4.93        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       11.77        27.12        13.87         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       36.13        29.56        20.94       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       13.32        41.23        28.18        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 
       53.16        52.08        30.38        15.58         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ 
       79.73         6.71        20.91        38.93        41.19        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87         4.70         5.82         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       16.31       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       60.92        66.97        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        31.99        31.96        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       48.72        62.14        60.56        16.83        56.52        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        53.06        45.86        46.29       114.38        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
        8.98        14.04        53.36        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       28.34         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN 
       37.94        36.43        22.59        20.28        12.43         3.78 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        22.75        14.96        11.47        13.48 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.15              0.72 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           111.39            165.17 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           29.850            26.545 
[1] "1.1 - 111.4 (29.9)" "0.7 - 165.2 (26.5)"
[1] "hr="     "2.7e+07"
D17V2, continuous
                   vv
clus                 T2  T3  T4
  9P GAIN MUTATED     2  28   1
  9P GAIN WILD-TYPE 186 253   9
D17V3, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T2               2               186
  T3              28               253
  T4               1                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    17  13
  9P GAIN WILD-TYPE 321  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     17   13
  9P GAIN WILD-TYPE  321   62
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              17               321
  1              13                62
[1] 2 2
[1] FALSE
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  29
  9P GAIN WILD-TYPE  12 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   29
  9P GAIN WILD-TYPE   12  439
                                        clus
vv                                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               2                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 29               439
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    14  15   1   0
  9P GAIN WILD-TYPE 296 123   4  15
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              14               296
  R1              15               123
  R2               1                 4
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, continuous
D17V8, continuous
D17V9, continuous
D17V10, continuous
D17V11, continuous
D17V12, continuous
D17V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         1     6
  9P GAIN WILD-TYPE     2                         6   140
D17V14, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   6               140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    47   0
  9Q GAIN WILD-TYPE 426   8
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               47               434 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                 8 
$`9Q GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5771 TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5526 
       35.01        13.02        33.01        33.11        19.56        38.76 
TCGA-EJ-7789 TCGA-EJ-8472 TCGA-EJ-A46G TCGA-EJ-A65F TCGA-FC-A4JI TCGA-G9-6356 
       18.15        24.85        21.96        18.41        13.45        47.15 
TCGA-G9-6373 TCGA-G9-7521 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8266 TCGA-HC-A4ZV 
       26.66        30.97        31.43        22.42         1.15         0.76 
TCGA-HC-A631 TCGA-HC-A8CY TCGA-J4-AATZ TCGA-KK-A59Z TCGA-KK-A7AU TCGA-KK-A8I4 
        1.78         9.53        13.55        86.40        58.36        67.99 
TCGA-V1-A8MJ TCGA-V1-A8WV TCGA-V1-A9OL TCGA-VN-A88K TCGA-VP-A872 TCGA-VP-A875 
       40.44        22.55        19.36        25.51       111.39        75.91 
TCGA-VP-A87D TCGA-VP-A87H TCGA-X4-A8KQ TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8SC 
       60.92        21.80        45.47        37.25        71.77        41.46 
TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WK TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L9 
       32.45        62.79        62.37        11.67        29.85        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9M4 TCGA-ZG-A9NI 
       19.17         3.78        16.96        17.98         4.34 

$`9Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5497 TCGA-EJ-5498 
       32.02         2.99        29.00        27.16        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 
       64.50        51.88        68.35        43.07        36.66        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.53        14.14        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        77.16        76.41        38.10        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       20.58        17.23        25.74        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V 
        4.31         4.77        28.41        15.42        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       46.16        50.70        49.35        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       40.31        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       30.84        17.85        24.56        19.36        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       15.88        22.36         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        4.93        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        14.37        20.28        11.77        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        5.85        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       44.68       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       52.93        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        20.94       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MK TCGA-V1-A8ML 
       11.90        13.32        41.23        28.18        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        15.58         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88L 
       17.75        49.87         4.70         5.82         8.84        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       16.31       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KS 
       66.97        53.36        42.94        44.88        14.76        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        31.99        31.96        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
        4.87        52.96        49.02        51.45        48.72        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        56.52        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH 
       45.86        46.29       114.38        71.34         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        60.99        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13         4.27        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC 
       22.59        12.43        19.04        12.16        22.75        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       11.47        13.48 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.76              0.72 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           111.39            165.17 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           25.510            27.005 
[1] "0.8 - 111.4 (25.5)" "0.7 - 165.2 (27.0)"
[1] "hr="     "7.8e+07"
D18V2, continuous
                   vv
clus                 T2  T3  T4
  9Q GAIN MUTATED     4  41   2
  9Q GAIN WILD-TYPE 184 240   8
D18V3, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T2               4               184
  T3              41               240
  T4               2                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    25  20
  9Q GAIN WILD-TYPE 313  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     25   20
  9Q GAIN WILD-TYPE  313   55
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              25               313
  1              20                55
[1] 2 2
[1] FALSE
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3  44
  9Q GAIN WILD-TYPE  11 424
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3   44
  9Q GAIN WILD-TYPE   11  424
                                        clus
vv                                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               3                11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 44               424
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    22  22   1   1
  9Q GAIN WILD-TYPE 288 116   4  14
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              22               288
  R1              22               116
  R2               1                 4
  RX               1                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"
D18V7, continuous
D18V8, continuous
D18V9, continuous
D18V10, continuous
D18V11, continuous
D18V12, continuous
D18V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         1     9
  9Q GAIN WILD-TYPE     2                         6   137
D18V14, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   9               137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    14   0
  10P GAIN WILD-TYPE 459   8
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                467 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  8 
$`10P GAIN MUTATED`
TCGA-EJ-5514 TCGA-EJ-8469 TCGA-G9-6499 TCGA-HC-7078 TCGA-HC-7231 TCGA-HC-7742 
       36.23        76.41        50.73        65.26         2.37         1.48 
TCGA-KK-A7AV TCGA-V1-A8WV TCGA-VP-A872 TCGA-YL-A9WH TCGA-YL-A9WY TCGA-ZG-A9LM 
       27.02        22.55       111.39        14.04        28.34        12.43 
TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       11.47         4.34 

$`10P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        77.16        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        64.18        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       30.94         3.68        19.76         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       13.55        27.12        13.87         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        15.58         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78        16.31        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        71.34        62.79         8.98        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       62.37        24.33        49.91         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
       10.13         4.27        11.67        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       22.59        20.28        19.17         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        13.48 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.48               0.72 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            111.39             165.17 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            24.785             26.660 
[1] "1.5 - 111.4 (24.8)" "0.7 - 165.2 (26.7)"
[1] "hr="     "2.6e+07"
D19V2, continuous
                    vv
clus                  T2  T3  T4
  10P GAIN MUTATED     3  11   0
  10P GAIN WILD-TYPE 185 270  10
D19V3, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T2                3                185
  T3               11                270
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     8   5
  10P GAIN WILD-TYPE 330  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8    5
  10P GAIN WILD-TYPE  330   70
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                8                330
  1                5                 70
[1] 2 2
[1] FALSE
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1  13
  10P GAIN WILD-TYPE  13 455
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   13
  10P GAIN WILD-TYPE   13  455
                                        clus
vv                                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  13                455
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED     8   4   0   2
  10P GAIN WILD-TYPE 302 134   5  13
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                8                302
  R1                4                134
  R2                0                  5
  RX                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, continuous
D19V8, continuous
D19V9, continuous
D19V10, continuous
D19V11, continuous
D19V12, continuous
D19V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0     5
  10P GAIN WILD-TYPE     2                         7   141
D19V14, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    5                141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    13   0
  10Q GAIN WILD-TYPE 460   8
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                468 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                  8 
$`10Q GAIN MUTATED`
TCGA-CH-5761 TCGA-CH-5788 TCGA-EJ-5514 TCGA-EJ-8469 TCGA-HC-7078 TCGA-HC-7231 
        0.92        26.99        36.23        76.41        65.26         2.37 
TCGA-HC-7742 TCGA-KK-A7AV TCGA-V1-A8WV TCGA-VP-A872 TCGA-YL-A8SQ TCGA-YL-A9WY 
        1.48        27.02        22.55       111.39        62.79        28.34 
TCGA-ZG-A9N3 
       11.47 

$`10Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        15.98         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        36.69        48.53        38.53        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
        3.68        19.76         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7232 
       28.54         0.79        28.60        40.08         1.68        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
       44.55         0.72         2.10        31.69        23.57         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AW 
       67.07        58.19         6.44        52.93        58.36        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 
       53.16        52.08        30.38        15.58         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78        16.31        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34         8.98        14.04        53.36        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       24.33        49.91         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
        4.27        11.67        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        22.75        17.98        14.96        13.48         4.34 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.92               0.72 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            111.39             165.17 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            27.020             26.365 
[1] "0.9 - 111.4 (27.0)" "0.7 - 165.2 (26.4)"
[1] "hr="     "2.6e+07"
D20V2, continuous
                    vv
clus                  T2  T3  T4
  10Q GAIN MUTATED     3  10   0
  10Q GAIN WILD-TYPE 185 271  10
D20V3, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T2                3                185
  T3               10                271
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     8   4
  10Q GAIN WILD-TYPE 330  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      8    4
  10Q GAIN WILD-TYPE  330   71
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                8                330
  1                4                 71
[1] 2 2
[1] FALSE
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  12
  10Q GAIN WILD-TYPE  13 456
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   12
  10Q GAIN WILD-TYPE   13  456
                                        clus
vv                                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  12                456
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED     8   3   0   2
  10Q GAIN WILD-TYPE 302 135   5  13
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                8                302
  R1                3                135
  R2                0                  5
  RX                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, continuous
D20V8, continuous
D20V9, continuous
D20V10, continuous
D20V11, continuous
D20V12, continuous
D20V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     6
  10Q GAIN WILD-TYPE     2                         7   140
D20V14, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    6                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    24   0
  11P GAIN WILD-TYPE 449   8
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                24                457 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  8 
$`11P GAIN MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-EJ-5495 TCGA-EJ-5511 TCGA-EJ-7784 TCGA-G9-7523 
       11.51        35.01        33.11        48.53        25.68        28.18 
TCGA-HC-8216 TCGA-HC-A76W TCGA-HI-7168 TCGA-J4-AATZ TCGA-KC-A7FA TCGA-KK-A6E8 
       22.42         7.00        78.61        13.55        19.66        58.19 
TCGA-KK-A8I4 TCGA-V1-A8WV TCGA-X4-A8KS TCGA-YL-A8HM TCGA-YL-A8SQ TCGA-YL-A9WH 
       67.99        22.55        32.19        48.72        62.79        14.04 
TCGA-YL-A9WI TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LS TCGA-ZG-A9M4 
       53.36        11.67        29.85        19.17        16.96        17.98 

$`11P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 
       32.02        33.01         2.99        29.00        27.16        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.77        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 
       52.93        38.96        27.91        30.97        35.34        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
        2.33         3.48         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        9.53        25.48        18.84        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       14.37        20.28        11.77        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
       49.25       113.33        67.07         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       36.13        29.56        20.94       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        15.58         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        53.36        42.94        44.88        14.76        45.47 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       25.48         4.87        52.96        49.02        51.45        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       71.34         8.98        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       28.34         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN 
       37.94        36.43        22.59        20.28        12.43         3.78 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        22.75        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              7.00               0.72 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             78.61             165.17 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             26.93              26.66 
[1] "7.0 - 78.6 (26.9)"  "0.7 - 165.2 (26.7)"
[1] "hr="     "2.6e+07"
D21V2, continuous
                    vv
clus                  T2  T3  T4
  11P GAIN MUTATED     3  19   2
  11P GAIN WILD-TYPE 185 262   8
D21V3, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T2                3                185
  T3               19                262
  T4                2                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    13  10
  11P GAIN WILD-TYPE 325  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     13   10
  11P GAIN WILD-TYPE  325   65
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               13                325
  1               10                 65
[1] 2 2
[1] FALSE
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  24
  11P GAIN WILD-TYPE  14 444
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   24
  11P GAIN WILD-TYPE   14  444
                                        clus
vv                                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  24                444
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    10  12   0   2
  11P GAIN WILD-TYPE 300 126   5  13
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               10                300
  R1               12                126
  R2                0                  5
  RX                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, continuous
D21V8, continuous
D21V9, continuous
D21V10, continuous
D21V11, continuous
D21V12, continuous
D21V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         1     4
  11P GAIN WILD-TYPE     2                         6   142
D21V14, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    4                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    27   0
  11Q GAIN WILD-TYPE 446   8
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                454 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  8 
$`11Q GAIN MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-EJ-5495 TCGA-EJ-5511 TCGA-EJ-7784 TCGA-EJ-8472 
       11.51        35.01        33.11        48.53        25.68        24.85 
TCGA-G9-7523 TCGA-HC-8216 TCGA-HC-A76W TCGA-HI-7168 TCGA-KC-A7FA TCGA-KK-A6E8 
       28.18        22.42         7.00        78.61        19.66        58.19 
TCGA-KK-A8I4 TCGA-KK-A8IK TCGA-V1-A8WV TCGA-X4-A8KS TCGA-YL-A8HM TCGA-YL-A8SB 
       67.99        51.39        22.55        32.19        48.72        56.52 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB 
       62.79        14.04        53.36        11.67        29.85        19.17 
TCGA-ZG-A9LS TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       16.96        17.98        11.47 

$`11Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 
       32.02        33.01         2.99        29.00        27.16        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 
       38.96        27.91        30.97        35.34        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        3.48         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
       49.25       113.33        67.07         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       36.13        29.56        20.94       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL 
       26.43        82.36        66.18       113.98        51.25        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 
       53.16        52.08        30.38        15.58         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XA-A8JR 
       53.36        42.94        44.88        14.76        45.47         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 
        4.87        52.96        49.02        51.45        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR 
       45.86        46.29        32.45       114.38        71.34         8.98 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13         4.27        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LU TCGA-ZG-A9LY 
       22.59        20.28        12.43         3.78        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        14.96        13.48         4.34 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              7.00               0.72 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             78.61             165.17 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            28.180             26.545 
[1] "7.0 - 78.6 (28.2)"  "0.7 - 165.2 (26.5)"
[1] "hr="     "2.7e+07"
D22V2, continuous
                    vv
clus                  T2  T3  T4
  11Q GAIN MUTATED     4  21   2
  11Q GAIN WILD-TYPE 184 260   8
D22V3, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T2                4                184
  T3               21                260
  T4                2                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    15  11
  11Q GAIN WILD-TYPE 323  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     15   11
  11Q GAIN WILD-TYPE  323   64
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               15                323
  1               11                 64
[1] 2 2
[1] FALSE
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  27
  11Q GAIN WILD-TYPE  14 441
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   27
  11Q GAIN WILD-TYPE   14  441
                                        clus
vv                                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  27                441
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    12  13   0   2
  11Q GAIN WILD-TYPE 298 125   5  13
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               12                298
  R1               13                125
  R2                0                  5
  RX                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, continuous
D22V8, continuous
D22V9, continuous
D22V10, continuous
D22V11, continuous
D22V12, continuous
D22V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         1     4
  11Q GAIN WILD-TYPE     2                         6   142
D22V14, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    4                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    13   0
  12P GAIN WILD-TYPE 460   8
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                13                468 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  8 
$`12P GAIN MUTATED`
TCGA-FC-A4JI TCGA-HC-8264 TCGA-J9-A8CL TCGA-KK-A8I7 TCGA-V1-A9OA TCGA-VP-A875 
       13.45         1.58        13.32        65.82        20.91        75.91 
TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-ZG-A9L0 
       21.80        37.25       114.38        62.79        14.04        11.67 
TCGA-ZG-A9LB 
       19.17 

$`12P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        15.42        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       17.95        22.32        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
       13.87         5.85        10.62        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
       67.99       101.79        21.96        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       30.38        15.58        22.55         6.64        58.39        79.73 
TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
        6.71        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      111.39       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       60.92        66.97        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        31.99        31.96        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       32.45        71.34         8.98        53.36        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       10.13         4.27        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       20.28        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.58               0.72 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            114.38             165.17 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            20.910             27.005 
[1] "1.6 - 114.4 (20.9)" "0.7 - 165.2 (27.0)"
[1] "hr="     "2.8e+07"
D23V2, continuous
                    vv
clus                  T2  T3  T4
  12P GAIN MUTATED     0  13   0
  12P GAIN WILD-TYPE 188 268  10
D23V3, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T2                0                188
  T3               13                268
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     5   5
  12P GAIN WILD-TYPE 333  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5    5
  12P GAIN WILD-TYPE  333   70
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                5                333
  1                5                 70
[1] 2 2
[1] FALSE
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  13
  12P GAIN WILD-TYPE  14 455
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   13
  12P GAIN WILD-TYPE   14  455
                                        clus
vv                                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  13                455
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED     3   9   1   0
  12P GAIN WILD-TYPE 307 129   4  15
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0                3                307
  R1                9                129
  R2                1                  4
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, continuous
D23V8, continuous
D23V9, continuous
D23V10, continuous
D23V11, continuous
D23V12, continuous
D23V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       0                         0     0
  12P GAIN WILD-TYPE     2                         7   146
D23V14, multiclass

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    16   0
  12Q GAIN WILD-TYPE 457   8
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                465 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  8 
$`12Q GAIN MUTATED`
TCGA-CH-5762 TCGA-EJ-A7NH TCGA-FC-A4JI TCGA-HC-8264 TCGA-J9-A8CL TCGA-KK-A8I7 
       44.02        15.58        13.45         1.58        13.32        65.82 
TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-ZG-A9L0 
       21.80        37.25       114.38        62.79        14.04        11.67 
TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LU TCGA-ZG-A9LY 
       29.85        19.17        19.04        12.16 

$`12Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04         0.92        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.62        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       21.96        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       60.92        66.97        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        31.99        31.96        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       32.45        71.34         8.98        53.36        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       10.13         4.27        37.94        36.43        22.59        20.28 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       12.43         3.78        16.96        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.58               0.72 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            114.38             165.17 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            19.105             27.020 
[1] "1.6 - 114.4 (19.1)" "0.7 - 165.2 (27.0)"
[1] "hr="     "2.8e+07"
D24V2, continuous
                    vv
clus                  T2  T3  T4
  12Q GAIN MUTATED     1  14   1
  12Q GAIN WILD-TYPE 187 267   9
D24V3, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T2                1                187
  T3               14                267
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     7   6
  12Q GAIN WILD-TYPE 331  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7    6
  12Q GAIN WILD-TYPE  331   69
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                7                331
  1                6                 69
[1] 2 2
[1] FALSE
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  16
  12Q GAIN WILD-TYPE  14 452
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   16
  12Q GAIN WILD-TYPE   14  452
                                        clus
vv                                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  16                452
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED     2  13   1   0
  12Q GAIN WILD-TYPE 308 125   4  15
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                2                308
  R1               13                125
  R2                1                  4
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, continuous
D24V8, continuous
D24V9, continuous
D24V10, continuous
D24V11, continuous
D24V12, continuous
D24V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       0                         0     1
  12Q GAIN WILD-TYPE     2                         7   145
D24V14, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5763         TCGA-CH-5764         TCGA-CH-5765 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5766         TCGA-CH-5767         TCGA-CH-5768 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5769         TCGA-CH-5771         TCGA-CH-5772 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5788         TCGA-CH-5789         TCGA-CH-5790 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5791         TCGA-CH-5792         TCGA-CH-5794 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5494         TCGA-EJ-5495         TCGA-EJ-5496 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5497         TCGA-EJ-5498         TCGA-EJ-5499 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5501         TCGA-EJ-5503         TCGA-EJ-5504 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5506         TCGA-EJ-5507 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"12Q GAIN WILD-TYPE" 

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     8   0
  13Q GAIN WILD-TYPE 465   8
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                473 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                  8 
$`13Q GAIN MUTATED`
TCGA-EJ-7784 TCGA-G9-7509 TCGA-KC-A7F6 TCGA-VP-A872 TCGA-YL-A8HO TCGA-YL-A8S8 
       25.68        52.93         8.65       111.39        71.77        62.14 
TCGA-ZG-A9L5 TCGA-ZG-A9N3 
       29.85        11.47 

$`13Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        23.90        38.37        25.87        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       13.87         5.85        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 
       52.08        30.38        15.58        22.55         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78        16.31        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S9 
        4.87        52.96        49.02        51.45        48.72        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
        4.27        11.67        37.94        36.43        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        13.48         4.34 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              8.65               0.72 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            111.39             165.17 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             41.39              26.43 
[1] "8.7 - 111.4 (41.4)" "0.7 - 165.2 (26.4)"
[1] "hr="     "9400000"
D25V2, continuous
                    vv
clus                  T2  T3  T4
  13Q GAIN MUTATED     3   4   1
  13Q GAIN WILD-TYPE 185 277   9
D25V3, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T2                3                185
  T3                4                277
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     5   2
  13Q GAIN WILD-TYPE 333  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    2
  13Q GAIN WILD-TYPE  333   73
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                5                333
  1                2                 73
[1] 2 2
[1] FALSE
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1   7
  13Q GAIN WILD-TYPE  13 461
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    7
  13Q GAIN WILD-TYPE   13  461
                                        clus
vv                                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   7                461
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED     4   4   0   0
  13Q GAIN WILD-TYPE 306 134   5  15
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                4                306
  R1                4                134
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, continuous
D25V8, continuous
D25V9, continuous
D25V10, continuous
D25V11, continuous
D25V12, continuous
D25V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         0     1
  13Q GAIN WILD-TYPE     2                         7   145
D25V14, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5527 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7115         TCGA-EJ-7123 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7125         TCGA-EJ-7314         TCGA-EJ-7315 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7317         TCGA-EJ-7321         TCGA-EJ-7327 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"13Q GAIN WILD-TYPE" 

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     8   1
  14Q GAIN WILD-TYPE 465   7
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                472 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                  7 
$`14Q GAIN MUTATED`
TCGA-CH-5772 TCGA-FC-A4JI TCGA-G9-A9S0 TCGA-HC-A631 TCGA-KK-A59Z TCGA-KK-A6E8 
       15.98        13.45        26.01         1.78        86.40        58.19 
TCGA-VP-A872 TCGA-YL-A8SK TCGA-ZG-A9LB 
      111.39        46.29        19.17 

$`14Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 
        1.02        15.06        24.03         2.04        13.02        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       15.42        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 
       30.97        35.34        28.18        32.68        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 
        1.58        15.88         1.15        22.36         0.76         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
       49.25       113.33        67.07         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 
       15.81        41.42        44.91        25.78        16.31        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM 
       37.94        36.43        29.85        22.59        20.28        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.78               0.72 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            111.39             165.17 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            26.010             26.825 
[1] "1.8 - 111.4 (26.0)" "0.7 - 165.2 (26.8)"
[1] "hr=" "8.3"
D26V2, continuous
                    vv
clus                  T2  T3  T4
  14Q GAIN MUTATED     3   6   0
  14Q GAIN WILD-TYPE 185 275  10
D26V3, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T2                3                185
  T3                6                275
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     6   2
  14Q GAIN WILD-TYPE 332  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6    2
  14Q GAIN WILD-TYPE  332   73
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                6                332
  1                2                 73
[1] 2 2
[1] FALSE
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1   8
  14Q GAIN WILD-TYPE  13 460
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    8
  14Q GAIN WILD-TYPE   13  460
                                        clus
vv                                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   8                460
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED     3   5   0   1
  14Q GAIN WILD-TYPE 307 133   5  14
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                3                307
  R1                5                133
  R2                0                  5
  RX                1                 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"
D26V7, continuous
D26V8, continuous
D26V9, continuous
D26V10, continuous
D26V11, continuous
D26V12, continuous
D26V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0     1
  14Q GAIN WILD-TYPE     2                         7   145
D26V14, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5788         TCGA-CH-5789         TCGA-CH-5790 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5791         TCGA-CH-5792         TCGA-CH-5794 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5494         TCGA-EJ-5495         TCGA-EJ-5496 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5497         TCGA-EJ-5498         TCGA-EJ-5499 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5501         TCGA-EJ-5503         TCGA-EJ-5504 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5506         TCGA-EJ-5507 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"14Q GAIN WILD-TYPE" 

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     6   0
  15Q GAIN WILD-TYPE 467   8
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                475 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 0                  8 
$`15Q GAIN MUTATED`
TCGA-EJ-5514 TCGA-G9-7525 TCGA-HC-8266 TCGA-V1-A8WV TCGA-VP-A875 TCGA-XK-AAIV 
       36.23        32.68         1.15        22.55        75.91        37.25 

$`15Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        30.97        35.34        28.18        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
       22.32         1.58        15.88        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        5.85        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       52.08        30.38        15.58         6.64        58.39        79.73 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
        6.71        20.91        38.93        41.19        19.36        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87         4.70         5.82         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       16.31       111.39       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
        4.27        11.67        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.15               0.72 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             75.91             165.17 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            34.455             26.430 
[1] "1.1 - 75.9 (34.5)"  "0.7 - 165.2 (26.4)"
[1] "hr="     "9100000"
D27V2, continuous
                    vv
clus                  T2  T3  T4
  15Q GAIN MUTATED     2   4   0
  15Q GAIN WILD-TYPE 186 277  10
D27V3, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T2                2                186
  T3                4                277
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     4   2
  15Q GAIN WILD-TYPE 334  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4    2
  15Q GAIN WILD-TYPE  334   73
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                4                334
  1                2                 73
[1] 2 2
[1] FALSE
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0   6
  15Q GAIN WILD-TYPE  14 462
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    6
  15Q GAIN WILD-TYPE   14  462
                                        clus
vv                                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   6                462
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     4   2   0   0
  15Q GAIN WILD-TYPE 306 136   5  15
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                4                306
  R1                2                136
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, continuous
D27V8, continuous
D27V9, continuous
D27V10, continuous
D27V11, continuous
D27V12, continuous
D27V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         0     1
  15Q GAIN WILD-TYPE     2                         7   145
D27V14, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"15Q GAIN WILD-TYPE" 

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    30   0
  16P GAIN WILD-TYPE 443   8
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                30                451 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  8 
$`16P GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-7328 TCGA-EJ-7783 TCGA-G9-6373 TCGA-G9-7521 
       35.01         0.92        27.68        25.87        26.66        30.97 
TCGA-HC-7213 TCGA-HC-7232 TCGA-HC-7742 TCGA-HC-A8CY TCGA-HI-7168 TCGA-J9-A52B 
       40.08        38.17         1.48         9.53        78.61        13.87 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8IF TCGA-KK-A8IK TCGA-QU-A6IL 
       20.94        67.99        65.82        26.43        51.39         3.19 
TCGA-QU-A6IO TCGA-V1-A8WV TCGA-V1-A9ZI TCGA-VP-A872 TCGA-XK-AAIV TCGA-YL-A8HM 
      122.17        22.55         4.70       111.39        37.25        48.72 
TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WX TCGA-ZG-A9L9 TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       71.34        14.04        49.91        20.28        11.47         4.34 

$`16P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        31.00         1.02         2.04 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       35.18        30.35         6.28        24.39        23.90        38.37 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       39.95        38.01        40.31        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       52.93        38.96        27.91        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7736 
        0.79        28.60         1.68         2.37        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.10        31.69        23.57         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 
        1.45         1.25         4.41         7.00         4.93        25.48 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       18.84        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       11.77        13.55        27.12         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 
       36.13        29.56       101.79        21.96        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH 
       63.48         2.73        67.43        69.27        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
      113.98        51.25        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
        5.69        41.00       140.19        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        15.58         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
        6.15        17.75        49.87         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78        16.31        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        51.45        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        46.29        32.45       114.38        62.79         8.98 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        60.99        62.37        24.33        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        29.85        22.59        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9ND 
       13.48 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.92               0.72 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            122.17             165.17 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             27.17              26.30 
[1] "0.9 - 122.2 (27.2)" "0.7 - 165.2 (26.3)"
[1] "hr="     "8.1e+07"
D28V2, continuous
                    vv
clus                  T2  T3  T4
  16P GAIN MUTATED     3  26   1
  16P GAIN WILD-TYPE 185 255   9
D28V3, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T2                3                185
  T3               26                255
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    16  11
  16P GAIN WILD-TYPE 322  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     16   11
  16P GAIN WILD-TYPE  322   64
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               16                322
  1               11                 64
[1] 2 2
[1] FALSE
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  29
  16P GAIN WILD-TYPE  13 439
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   29
  16P GAIN WILD-TYPE   13  439
                                        clus
vv                                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  29                439
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    17  13   0   0
  16P GAIN WILD-TYPE 293 125   5  15
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               17                293
  R1               13                125
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, continuous
D28V8, continuous
D28V9, continuous
D28V10, continuous
D28V11, continuous
D28V12, continuous
D28V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       0                         0     9
  16P GAIN WILD-TYPE     2                         7   137
D28V14, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    9                137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     8   0
  16Q GAIN WILD-TYPE 465   8
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                473 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 0                  8 
$`16Q GAIN MUTATED`
TCGA-CH-5761 TCGA-EJ-7328 TCGA-G9-6373 TCGA-HC-7232 TCGA-QU-A6IL TCGA-YL-A8HM 
        0.92        27.68        26.66        38.17         3.19        48.72 
TCGA-YL-A9WH TCGA-ZG-A9NI 
       14.04         4.34 

$`16Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       27.09        35.18        30.35         6.28        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 
        3.32        40.18        39.95        38.01        40.31        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        1.68         2.37        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        37.25        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        51.45        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
        8.98        53.36        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       28.34         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       22.75        17.98        14.96        11.47        13.48 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.92               0.72 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             48.72             165.17 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             20.35              26.99 
[1] "0.9 - 48.7 (20.4)"  "0.7 - 165.2 (27.0)"
[1] "hr="     "3300000"
D29V2, continuous
                    vv
clus                  T2  T3  T4
  16Q GAIN MUTATED     1   7   0
  16Q GAIN WILD-TYPE 187 274  10
D29V3, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T2                1                187
  T3                7                274
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     5   1
  16Q GAIN WILD-TYPE 333  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5    1
  16Q GAIN WILD-TYPE  333   74
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                5                333
  1                1                 74
[1] 2 2
[1] FALSE
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0   8
  16Q GAIN WILD-TYPE  14 460
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    8
  16Q GAIN WILD-TYPE   14  460
                                        clus
vv                                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   8                460
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED     6   2   0   0
  16Q GAIN WILD-TYPE 304 136   5  15
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                6                304
  R1                2                136
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, continuous
D29V8, continuous
D29V9, continuous
D29V10, continuous
D29V11, continuous
D29V12, continuous
D29V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         0     4
  16Q GAIN WILD-TYPE     2                         7   142
D29V14, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    4                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED     7   0
  17P GAIN WILD-TYPE 466   8
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                474 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                  8 
$`17P GAIN MUTATED`
TCGA-2A-A8VT TCGA-EJ-5527 TCGA-HC-8216 TCGA-TP-A8TT TCGA-V1-A8WV TCGA-XK-AAIV 
       32.71        39.75        22.42        11.90        22.55        37.25 
TCGA-YL-A9WY 
       28.34 

$`17P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        43.07        36.66        38.76        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 
       30.84        17.85        24.56        31.43        19.36        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        5.85        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
      122.17        86.14        18.12        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       30.38        15.58         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       49.91         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             11.90               0.72 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             39.75             165.17 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            28.340             26.545 
[1] "11.9 - 39.8 (28.3)" "0.7 - 165.2 (26.5)"
[1] "hr="     "3400000"
D30V2, continuous
                    vv
clus                  T2  T3  T4
  17P GAIN MUTATED     0   6   1
  17P GAIN WILD-TYPE 188 275   9
D30V3, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T2                0                188
  T3                6                275
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     3   4
  17P GAIN WILD-TYPE 335  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    4
  17P GAIN WILD-TYPE  335   71
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                3                335
  1                4                 71
[1] 2 2
[1] FALSE
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0   7
  17P GAIN WILD-TYPE  14 461
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    7
  17P GAIN WILD-TYPE   14  461
                                        clus
vv                                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   7                461
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     4   3   0   0
  17P GAIN WILD-TYPE 306 135   5  15
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                4                306
  R1                3                135
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, continuous
D30V8, continuous
D30V9, continuous
D30V10, continuous
D30V11, continuous
D30V12, continuous
D30V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       0                         0     1
  17P GAIN WILD-TYPE     2                         7   145
D30V14, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5530 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HI-7171 
"17P GAIN WILD-TYPE" 

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    10   0
  17Q GAIN WILD-TYPE 463   8
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                10                471 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                  8 
$`17Q GAIN MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-EJ-5527 TCGA-G9-7521 TCGA-HC-8216 TCGA-KK-A8I6 
       32.71        11.51        39.75        30.97        22.42        21.96 
TCGA-TP-A8TT TCGA-V1-A8WV TCGA-XK-AAIV TCGA-YL-A9WY 
       11.90        22.55        37.25        28.34 

$`17Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
       13.02        35.01        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       43.07        36.66        38.76        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 
       64.18        50.73        52.93        38.96        27.91        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        31.43        19.36        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       11.77        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        15.58         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        31.99        31.96        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX 
       60.99        62.37        24.33        49.91         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             11.51               0.72 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             39.75             165.17 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            25.445             26.660 
[1] "11.5 - 39.8 (25.4)" "0.7 - 165.2 (26.7)"
[1] "hr="     "9200000"
D31V2, continuous
                    vv
clus                  T2  T3  T4
  17Q GAIN MUTATED     0   9   1
  17Q GAIN WILD-TYPE 188 272   9
D31V3, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T2                0                188
  T3                9                272
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     5   5
  17Q GAIN WILD-TYPE 333  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    5
  17Q GAIN WILD-TYPE  333   70
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                5                333
  1                5                 70
[1] 2 2
[1] FALSE
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  10
  17Q GAIN WILD-TYPE  14 458
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   10
  17Q GAIN WILD-TYPE   14  458
                                        clus
vv                                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  10                458
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED     6   4   0   0
  17Q GAIN WILD-TYPE 304 134   5  15
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                6                304
  R1                4                134
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, continuous
D31V8, continuous
D31V9, continuous
D31V10, continuous
D31V11, continuous
D31V12, continuous
D31V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         0     1
  17Q GAIN WILD-TYPE     2                         7   145
D31V14, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5530 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"17Q GAIN WILD-TYPE" 

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    17   0
  18P GAIN WILD-TYPE 456   8
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                464 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  8 
$`18P GAIN MUTATED`
TCGA-EJ-5495 TCGA-EJ-5527 TCGA-FC-A4JI TCGA-G9-6329 TCGA-G9-6499 TCGA-G9-7521 
       33.11        39.75        13.45        41.62        50.73        30.97 
TCGA-HC-7742 TCGA-HC-8216 TCGA-J9-A52E TCGA-KK-A8I4 TCGA-V1-A8WL TCGA-VP-A875 
        1.48        22.42        10.62        67.99        52.08        75.91 
TCGA-XK-AAJT TCGA-YL-A9WY TCGA-ZG-A9KY TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       47.15        28.34         4.27        17.98        11.47 

$`18P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       27.16        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        43.07        36.66        38.76        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 
       22.36        17.23        16.24         1.78        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       52.93        38.96        27.91        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
       44.55         0.72         2.10        31.69        23.57         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
       13.87         5.85        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN 
       40.44        16.70        14.73        39.29        53.16        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      111.39       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        53.36        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       37.25        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        62.37        24.33        49.91 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC 
        3.78        16.96        19.04        12.16        22.75        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              1.48               0.72 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             75.91             165.17 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            30.970             26.365 
[1] "1.5 - 75.9 (31.0)"  "0.7 - 165.2 (26.4)"
[1] "hr="     "2.6e+07"
D32V2, continuous
                    vv
clus                  T2  T3  T4
  18P GAIN MUTATED     1  15   1
  18P GAIN WILD-TYPE 187 266   9
D32V3, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T2                1                187
  T3               15                266
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     8   7
  18P GAIN WILD-TYPE 330  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    7
  18P GAIN WILD-TYPE  330   68
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                8                330
  1                7                 68
[1] 2 2
[1] FALSE
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  17
  18P GAIN WILD-TYPE  14 451
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   17
  18P GAIN WILD-TYPE   14  451
                                        clus
vv                                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  17                451
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    11   6   0   0
  18P GAIN WILD-TYPE 299 132   5  15
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               11                299
  R1                6                132
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, continuous
D32V8, continuous
D32V9, continuous
D32V10, continuous
D32V11, continuous
D32V12, continuous
D32V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         0     5
  18P GAIN WILD-TYPE     2                         7   141
D32V14, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    5                141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     8   0
  18Q GAIN WILD-TYPE 465   8
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                473 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  8 
$`18Q GAIN MUTATED`
TCGA-EJ-5527 TCGA-G9-6499 TCGA-HC-8216 TCGA-J9-A52E TCGA-KK-A8I4 TCGA-V1-A8WL 
       39.75        50.73        22.42        10.62        67.99        52.08 
TCGA-VP-A875 TCGA-ZG-A9M4 
       75.91        17.98 

$`18Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 
       51.88        68.35        43.07        36.66        38.76        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 
       30.84        17.85        24.56        31.43        19.36        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
        5.85        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 
       32.84        34.95        36.13        29.56        20.94       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WS 
       16.70        14.73        39.29        53.16        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       28.34         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        14.96        11.47        13.48         4.34 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             10.62               0.72 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             75.91             165.17 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             45.24              26.43 
[1] "10.6 - 75.9 (45.2)" "0.7 - 165.2 (26.4)"
[1] "hr="     "9300000"
D33V2, continuous
                    vv
clus                  T2  T3  T4
  18Q GAIN MUTATED     0   8   0
  18Q GAIN WILD-TYPE 188 273  10
D33V3, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T2                0                188
  T3                8                273
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     6   2
  18Q GAIN WILD-TYPE 332  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6    2
  18Q GAIN WILD-TYPE  332   73
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                6                332
  1                2                 73
[1] 2 2
[1] FALSE
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   8
  18Q GAIN WILD-TYPE  14 460
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    8
  18Q GAIN WILD-TYPE   14  460
                                        clus
vv                                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   8                460
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     6   2   0   0
  18Q GAIN WILD-TYPE 304 136   5  15
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                6                304
  R1                2                136
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, continuous
D33V8, continuous
D33V9, continuous
D33V10, continuous
D33V11, continuous
D33V12, continuous
D33V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0     2
  18Q GAIN WILD-TYPE     2                         7   144
D33V14, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                153 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5530 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-H9-7775         TCGA-HC-7075         TCGA-HC-7077 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7078         TCGA-HC-7079         TCGA-HC-7080 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7081         TCGA-HC-7209         TCGA-HC-7210 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7232 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7233         TCGA-HC-7736         TCGA-HC-7737 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HI-7168 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    11   0
  19P GAIN WILD-TYPE 462   8
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                470 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  8 
$`19P GAIN MUTATED`
TCGA-CH-5751 TCGA-HC-7213 TCGA-KK-A7B4 TCGA-KK-A8ID TCGA-V1-A8WV TCGA-VP-A875 
       35.01        40.08        20.94        69.27        22.55        75.91 
TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A9WL TCGA-ZG-A9L5 TCGA-ZG-A9N3 
       71.77        56.52        24.33        29.85        11.47 

$`19P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       28.60         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       13.87         5.85        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
       63.48         2.73        67.43        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       30.38        15.58         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      111.39       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        53.36        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       37.25        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        51.45        48.72        62.14        60.56        16.83 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        60.99        62.37        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             11.47               0.72 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             75.91             165.17 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            35.010             26.365 
[1] "11.5 - 75.9 (35.0)" "0.7 - 165.2 (26.4)"
[1] "hr="     "2.6e+07"
D34V2, continuous
                    vv
clus                  T2  T3  T4
  19P GAIN MUTATED     0   9   2
  19P GAIN WILD-TYPE 188 272   8
D34V3, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T2                0                188
  T3                9                272
  T4                2                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     5   6
  19P GAIN WILD-TYPE 333  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      5    6
  19P GAIN WILD-TYPE  333   69
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                5                333
  1                6                 69
[1] 2 2
[1] FALSE
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  11
  19P GAIN WILD-TYPE  14 457
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   11
  19P GAIN WILD-TYPE   14  457
                                        clus
vv                                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  11                457
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED     4   7   0   0
  19P GAIN WILD-TYPE 306 131   5  15
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                4                306
  R1                7                131
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, continuous
D34V8, continuous
D34V9, continuous
D34V10, continuous
D34V11, continuous
D34V12, continuous
D34V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       0                         0     2
  19P GAIN WILD-TYPE     2                         7   144
D34V14, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                153 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5752         TCGA-CH-5753 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5754         TCGA-CH-5761         TCGA-CH-5762 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5763         TCGA-CH-5764         TCGA-CH-5765 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5766         TCGA-CH-5767         TCGA-CH-5768 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5769         TCGA-CH-5771         TCGA-CH-5772 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5788         TCGA-CH-5789         TCGA-CH-5790 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5791         TCGA-CH-5792         TCGA-CH-5794 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5494         TCGA-EJ-5495         TCGA-EJ-5496 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5497         TCGA-EJ-5498         TCGA-EJ-5499 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5501         TCGA-EJ-5503         TCGA-EJ-5504 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5506         TCGA-EJ-5507 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7232 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7233         TCGA-HC-7736         TCGA-HC-7737 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HI-7168 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    11   0
  19Q GAIN WILD-TYPE 462   8
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                470 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  8 
$`19Q GAIN MUTATED`
TCGA-CH-5751 TCGA-HC-7213 TCGA-HI-7168 TCGA-KK-A7B4 TCGA-KK-A8ID TCGA-V1-A8WV 
       35.01        40.08        78.61        20.94        69.27        22.55 
TCGA-VP-A875 TCGA-YL-A8HO TCGA-YL-A8SB TCGA-ZG-A9L5 TCGA-ZG-A9N3 
       75.91        71.77        56.52        29.85        11.47 

$`19Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       28.60         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        9.53        25.48        18.84        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        5.85        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 
       49.94        32.84        34.95        36.13        29.56        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
        2.73        67.43        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       15.58         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC 
       51.45        48.72        62.14        60.56        16.83        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             11.47               0.72 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             78.61             165.17 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             40.08              26.17 
[1] "11.5 - 78.6 (40.1)" "0.7 - 165.2 (26.2)"
[1] "hr="     "2.6e+07"
D35V2, continuous
                    vv
clus                  T2  T3  T4
  19Q GAIN MUTATED     0   9   2
  19Q GAIN WILD-TYPE 188 272   8
D35V3, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T2                0                188
  T3                9                272
  T4                2                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     5   6
  19Q GAIN WILD-TYPE 333  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5    6
  19Q GAIN WILD-TYPE  333   69
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                5                333
  1                6                 69
[1] 2 2
[1] FALSE
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0  11
  19Q GAIN WILD-TYPE  14 457
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   11
  19Q GAIN WILD-TYPE   14  457
                                        clus
vv                                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  11                457
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED     4   7   0   0
  19Q GAIN WILD-TYPE 306 131   5  15
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                4                306
  R1                7                131
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, continuous
D35V8, continuous
D35V9, continuous
D35V10, continuous
D35V11, continuous
D35V12, continuous
D35V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       0                         0     3
  19Q GAIN WILD-TYPE     2                         7   143
D35V14, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    3                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    24   0
  20P GAIN WILD-TYPE 449   8
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                24                457 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 0                  8 
$`20P GAIN MUTATED`
TCGA-4L-AA1F TCGA-EJ-A65M TCGA-G9-6499 TCGA-HI-7168 TCGA-J9-A52E TCGA-J9-A8CN 
       11.51         7.56        50.73        78.61        10.62        40.67 
TCGA-KC-A7FA TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A8I4 TCGA-KK-A8IF TCGA-V1-A9O5 
       19.66        58.19        49.94        67.99        26.43        58.39 
TCGA-V1-A9OL TCGA-VP-A875 TCGA-VP-A87D TCGA-XJ-A83H TCGA-XK-AAIV TCGA-YL-A8HM 
       19.36        75.91        60.92        42.08        37.25        48.72 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       14.04        53.36        19.04        22.75        17.98        11.47 

$`20P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       14.83        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        64.18        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        15.22        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       44.35        43.66        21.86         8.65         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       67.07         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       51.68        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
        2.73        67.43        69.27        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       15.58        22.55         6.64        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       38.93        41.19        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 
       41.42        44.91        25.78        16.31       111.39       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H 
       97.41        23.93        85.18        55.56        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
        3.91        37.05        38.04        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        51.45        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
        8.98        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       37.94        36.43        29.85        22.59        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND 
       12.43         3.78        16.96        12.16        14.96        13.48 
TCGA-ZG-A9NI 
        4.34 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              7.56               0.72 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             78.61             165.17 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             38.96              26.30 
[1] "7.6 - 78.6 (39.0)"  "0.7 - 165.2 (26.3)"
[1] "hr="     "2.7e+07"
D36V2, continuous
                    vv
clus                  T2  T3  T4
  20P GAIN MUTATED     3  20   1
  20P GAIN WILD-TYPE 185 261   9
D36V3, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T2                3                185
  T3               20                261
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    14   8
  20P GAIN WILD-TYPE 324  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     14    8
  20P GAIN WILD-TYPE  324   67
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               14                324
  1                8                 67
[1] 2 2
[1] FALSE
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     0  24
  20P GAIN WILD-TYPE  14 444
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0   24
  20P GAIN WILD-TYPE   14  444
                                        clus
vv                                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  24                444
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED    12  10   0   1
  20P GAIN WILD-TYPE 298 128   5  14
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               12                298
  R1               10                128
  R2                0                  5
  RX                1                 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"
D36V7, continuous
D36V8, continuous
D36V9, continuous
D36V10, continuous
D36V11, continuous
D36V12, continuous
D36V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       0                         0     2
  20P GAIN WILD-TYPE     2                         7   144
D36V14, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                153 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5527 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7115         TCGA-EJ-7123 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7125         TCGA-EJ-7314         TCGA-EJ-7315 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7317         TCGA-EJ-7321         TCGA-EJ-7327 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-FC-7961 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6496         TCGA-H9-7775         TCGA-HC-7075 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    27   0
  20Q GAIN WILD-TYPE 446   8
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                27                454 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  8 
$`20Q GAIN MUTATED`
TCGA-4L-AA1F TCGA-CH-5762 TCGA-EJ-5518 TCGA-EJ-7314 TCGA-EJ-A65M TCGA-G9-6499 
       11.51        44.02        52.27        37.81         7.56        50.73 
TCGA-HI-7168 TCGA-J9-A52E TCGA-J9-A8CN TCGA-KK-A6E8 TCGA-KK-A8I4 TCGA-KK-A8IF 
       78.61        10.62        40.67        58.19        67.99        26.43 
TCGA-V1-A9O5 TCGA-V1-A9OL TCGA-VP-A875 TCGA-VP-A87D TCGA-XJ-A83H TCGA-XK-AAIV 
       58.39        19.36        75.91        60.92        42.08        37.25 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A9LM TCGA-ZG-A9LU 
       48.72        62.14        14.04        53.36        12.43        19.04 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       22.75        17.98        11.47 

$`20Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        0.92        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       46.55        47.80        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC 
       13.71        18.41        21.90        14.83        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.77        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 
       25.15        27.29        58.22        56.75        64.18        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        7.00         4.93         9.53        25.48        18.84        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
       27.12        13.87         5.85        13.32        15.22        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP 
       67.59       115.13        49.25       113.33        67.07         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 
       32.84        34.95        36.13        29.56        20.94       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       67.43        69.27        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       22.55         6.64        79.73         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       41.19        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78        16.31       111.39       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       23.93        85.18        55.56        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       37.05        38.04        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       49.02        51.45        71.77        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ 
       32.45       114.38        71.34        62.79         8.98        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS 
       29.85        22.59        20.28        19.17         3.78        16.96 
TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        14.96        13.48         4.34 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              7.56               0.72 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             78.61             165.17 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            40.670             26.025 
[1] "7.6 - 78.6 (40.7)"  "0.7 - 165.2 (26.0)"
[1] "hr="     "2.7e+07"
D37V2, continuous
                    vv
clus                  T2  T3  T4
  20Q GAIN MUTATED     3  22   2
  20Q GAIN WILD-TYPE 185 259   8
D37V3, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T2                3                185
  T3               22                259
  T4                2                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    16   9
  20Q GAIN WILD-TYPE 322  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     16    9
  20Q GAIN WILD-TYPE  322   66
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               16                322
  1                9                 66
[1] 2 2
[1] FALSE
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     0  27
  20Q GAIN WILD-TYPE  14 441
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0   27
  20Q GAIN WILD-TYPE   14  441
                                        clus
vv                                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  27                441
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED    12  13   0   1
  20Q GAIN WILD-TYPE 298 125   5  14
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               12                298
  R1               13                125
  R2                0                  5
  RX                1                 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"
D37V7, continuous
D37V8, continuous
D37V9, continuous
D37V10, continuous
D37V11, continuous
D37V12, continuous
D37V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       0                         0     5
  20Q GAIN WILD-TYPE     2                         7   141
D37V14, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    5                141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    20   0
  21Q GAIN WILD-TYPE 453   8
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                20                461 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                  8 
$`21Q GAIN MUTATED`
TCGA-EJ-7784 TCGA-G9-6499 TCGA-HI-7168 TCGA-J9-A52E TCGA-KK-A59Z TCGA-KK-A7B4 
       25.68        50.73        78.61        10.62        86.40        20.94 
TCGA-KK-A8I4 TCGA-KK-A8IA TCGA-V1-A8WV TCGA-V1-A9Z7 TCGA-VP-A872 TCGA-VP-A875 
       67.99        63.48        22.55         4.27       111.39        75.91 
TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A9WH TCGA-YL-A9WI 
       21.80        37.25        71.77        62.14        14.04        53.36 
TCGA-ZG-A9L0 TCGA-ZG-A9LB 
       11.67        19.17 

$`21Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        23.90        38.37        25.87        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        9.53        25.48        18.84        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
        5.85        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        29.56       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       31.79        32.91         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 
       53.16        52.08        30.38        15.58         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       12.20        15.65         8.42         5.59         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87         4.70         5.82         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       16.31       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       60.92        66.97        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        31.99        31.96        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       48.72        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       71.34        62.79         8.98        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
        4.27        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       12.43         3.78        16.96        19.04        12.16        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              4.27               0.72 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            111.39             165.17 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             43.99              26.43 
[1] "4.3 - 111.4 (44.0)" "0.7 - 165.2 (26.4)"
[1] "hr="     "2.8e+07"
D38V2, continuous
                    vv
clus                  T2  T3  T4
  21Q GAIN MUTATED     2  18   0
  21Q GAIN WILD-TYPE 186 263  10
D38V3, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T2                2                186
  T3               18                263
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    12   8
  21Q GAIN WILD-TYPE 326  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     12    8
  21Q GAIN WILD-TYPE  326   67
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               12                326
  1                8                 67
[1] 2 2
[1] FALSE
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  19
  21Q GAIN WILD-TYPE  13 449
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   19
  21Q GAIN WILD-TYPE   13  449
                                        clus
vv                                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  19                449
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    10   8   1   1
  21Q GAIN WILD-TYPE 300 130   4  14
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               10                300
  R1                8                130
  R2                1                  4
  RX                1                 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"
D38V7, continuous
D38V8, continuous
D38V9, continuous
D38V10, continuous
D38V11, continuous
D38V12, continuous
D38V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         0     3
  21Q GAIN WILD-TYPE     2                         7   143
D38V14, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    3                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     4   0
  22Q GAIN WILD-TYPE 469   8
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                477 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  8 
$`22Q GAIN MUTATED`
TCGA-EJ-5514 TCGA-VP-A876 TCGA-ZG-A9L0 TCGA-ZG-A9LZ 
       36.23       109.58        11.67        22.75 

$`22Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        58.39        79.73         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       111.39        75.91 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13         4.27        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC 
        3.78        16.96        19.04        12.16        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             11.67               0.72 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            109.58             165.17 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             29.49              26.66 
[1] "11.7 - 109.6 (29.5)" "0.7 - 165.2 (26.7)" 
[1] "hr="     "3300000"
D39V2, continuous
                    vv
clus                  T2  T3  T4
  22Q GAIN MUTATED     2   2   0
  22Q GAIN WILD-TYPE 186 279  10
D39V3, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T2                2                186
  T3                2                279
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3   1
  22Q GAIN WILD-TYPE 335  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    1
  22Q GAIN WILD-TYPE  335   74
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                3                335
  1                1                 74
[1] 2 2
[1] FALSE
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0   4
  22Q GAIN WILD-TYPE  14 464
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    4
  22Q GAIN WILD-TYPE   14  464
                                        clus
vv                                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   4                464
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED     2   2   0   0
  22Q GAIN WILD-TYPE 308 136   5  15
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                2                308
  R1                2                136
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, continuous
D39V8, continuous
D39V9, continuous
D39V10, continuous
D39V11, continuous
D39V12, continuous
D39V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         0     1
  22Q GAIN WILD-TYPE     2                         7   145
D39V14, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"22Q GAIN WILD-TYPE" 

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED     6   0
  XP GAIN WILD-TYPE 467   8
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6               475 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 8 
$`XP GAIN MUTATED`
TCGA-HC-A4ZV TCGA-J9-A8CM TCGA-VP-A87H TCGA-XK-AAJA TCGA-YL-A8S8 TCGA-ZG-A9L5 
        0.76        15.22        21.80        30.58        62.14        29.85 

$`XP GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN 
       27.12        13.87         5.85        10.62        13.32        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        45.86        46.29        32.45       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         8.98        14.04        53.36        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
       10.13         4.27        11.67        37.94        36.43        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.76              0.72 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            62.14            165.17 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           25.825            26.660 
[1] "0.8 - 62.1 (25.8)"  "0.7 - 165.2 (26.7)"
[1] "hr="     "9100000"
D40V2, continuous
                   vv
clus                 T2  T3  T4
  XP GAIN MUTATED     0   5   1
  XP GAIN WILD-TYPE 188 276   9
D40V3, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T2               0               188
  T3               5               276
  T4               1                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     4   2
  XP GAIN WILD-TYPE 334  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      4    2
  XP GAIN WILD-TYPE  334   73
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               4               334
  1               2                73
[1] 2 2
[1] FALSE
D40V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0   6
  XP GAIN WILD-TYPE  14 462
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0    6
  XP GAIN WILD-TYPE   14  462
                                        clus
vv                                       XP GAIN MUTATED XP GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  6               462
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED     1   4   1   0
  XP GAIN WILD-TYPE 309 134   4  15
D40V6, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0               1               309
  R1               4               134
  R2               1                 4
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, continuous
D40V8, continuous
D40V9, continuous
D40V10, continuous
D40V11, continuous
D40V12, continuous
D40V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         0     0
  XP GAIN WILD-TYPE     2                         7   146
D40V14, multiclass

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     6   0
  XQ GAIN WILD-TYPE 467   8
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6               475 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 8 
$`XQ GAIN MUTATED`
TCGA-HC-A4ZV TCGA-J9-A8CM TCGA-VP-A87H TCGA-XK-AAJA TCGA-YL-A8S8 TCGA-ZG-A9L5 
        0.76        15.22        21.80        30.58        62.14        29.85 

$`XQ GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN 
       27.12        13.87         5.85        10.62        13.32        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        45.86        46.29        32.45       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         8.98        14.04        53.36        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
       10.13         4.27        11.67        37.94        36.43        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.76              0.72 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            62.14            165.17 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           25.825            26.660 
[1] "0.8 - 62.1 (25.8)"  "0.7 - 165.2 (26.7)"
[1] "hr="     "9100000"
D41V2, continuous
                   vv
clus                 T2  T3  T4
  XQ GAIN MUTATED     0   5   1
  XQ GAIN WILD-TYPE 188 276   9
D41V3, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T2               0               188
  T3               5               276
  T4               1                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     4   2
  XQ GAIN WILD-TYPE 334  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4    2
  XQ GAIN WILD-TYPE  334   73
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               4               334
  1               2                73
[1] 2 2
[1] FALSE
D41V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0   6
  XQ GAIN WILD-TYPE  14 462
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    6
  XQ GAIN WILD-TYPE   14  462
                                        clus
vv                                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  6               462
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED     1   4   1   0
  XQ GAIN WILD-TYPE 309 134   4  15
D41V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               1               309
  R1               4               134
  R2               1                 4
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, continuous
D41V8, continuous
D41V9, continuous
D41V10, continuous
D41V11, continuous
D41V12, continuous
D41V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         0     0
  XQ GAIN WILD-TYPE     2                         7   146
D41V14, multiclass

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    21   0
  1P LOSS WILD-TYPE 452   8
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               460 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                 8 
$`1P LOSS MUTATED`
TCGA-EJ-7784 TCGA-G9-6361 TCGA-HC-7213 TCGA-HI-7168 TCGA-J9-A8CL TCGA-KK-A59Z 
       25.68        46.52        40.08        78.61        13.32        86.40 
TCGA-KK-A6E0 TCGA-KK-A6E6 TCGA-KK-A8IG TCGA-KK-A8IK TCGA-M7-A725 TCGA-V1-A8WV 
       30.02       113.33        82.36        51.39        18.84        22.55 
TCGA-VP-AA1N TCGA-YL-A8SJ TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WL TCGA-ZG-A9KY 
       44.88        45.86        62.79        14.04        24.33         4.27 
TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LZ 
       20.28        12.43        22.75 

$`1P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        23.90        38.37        25.87        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       49.35        47.15        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.62        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY 
        8.88        11.57       113.10        56.28        44.68       115.86 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 
       54.54       165.17        67.59       115.13        49.25        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18       113.98        51.25        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       15.58         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       60.92        66.97        21.80        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        53.06        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ 
       32.45       114.38        71.34         8.98        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       62.37        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       10.13        11.67        37.94        36.43        29.85        22.59 
TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 
       19.17         3.78        16.96        19.04        12.16        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             4.27              0.72 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           113.33            165.17 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           30.020            26.545 
[1] "4.3 - 113.3 (30.0)" "0.7 - 165.2 (26.5)"
[1] "hr="     "2.7e+07"
D42V2, continuous
                   vv
clus                 T2  T3  T4
  1P LOSS MUTATED     3  17   1
  1P LOSS WILD-TYPE 185 264   9
D42V3, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T2               3               185
  T3              17               264
  T4               1                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    15   5
  1P LOSS WILD-TYPE 323  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     15    5
  1P LOSS WILD-TYPE  323   70
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              15               323
  1               5                70
[1] 2 2
[1] FALSE
D42V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  21
  1P LOSS WILD-TYPE  14 447
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   21
  1P LOSS WILD-TYPE   14  447
                                        clus
vv                                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 21               447
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    11  10   0   0
  1P LOSS WILD-TYPE 299 128   5  15
D42V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              11               299
  R1              10               128
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, continuous
D42V8, continuous
D42V9, continuous
D42V10, continuous
D42V11, continuous
D42V12, continuous
D42V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       0                         0     4
  1P LOSS WILD-TYPE     2                         7   142
D42V14, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   4               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     6   0
  1Q LOSS WILD-TYPE 467   8
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6               475 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                 8 
$`1Q LOSS MUTATED`
TCGA-G9-6361 TCGA-J9-A8CL TCGA-KK-A8IG TCGA-YL-A8SQ TCGA-ZG-A9L9 TCGA-ZG-A9LM 
       46.52        13.32        82.36        62.79        20.28        12.43 

$`1Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       50.70        49.35        47.15        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN 
       27.12        13.87         5.85        10.62        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 
       52.08        30.38        15.58        22.55         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        71.34         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       29.85        22.59        19.17         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            12.43              0.72 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            82.36            165.17 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            33.40             26.66 
[1] "12.4 - 82.4 (33.4)" "0.7 - 165.2 (26.7)"
[1] "hr="     "9200000"
D43V2, continuous
                   vv
clus                 T2  T3  T4
  1Q LOSS MUTATED     0   6   0
  1Q LOSS WILD-TYPE 188 275  10
D43V3, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T2               0               188
  T3               6               275
  T4               0                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3   2
  1Q LOSS WILD-TYPE 335  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    2
  1Q LOSS WILD-TYPE  335   73
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               3               335
  1               2                73
[1] 2 2
[1] FALSE
D43V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   6
  1Q LOSS WILD-TYPE  14 462
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    6
  1Q LOSS WILD-TYPE   14  462
                                        clus
vv                                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  6               462
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED     1   5   0   0
  1Q LOSS WILD-TYPE 309 133   5  15
D43V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               1               309
  R1               5               133
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, continuous
D43V8, continuous
D43V9, continuous
D43V10, continuous
D43V11, continuous
D43V12, continuous
D43V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0     1
  1Q LOSS WILD-TYPE     2                         7   145
D43V14, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    14   1
  2P LOSS WILD-TYPE 459   7
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               466 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                 7 
$`2P LOSS MUTATED`
TCGA-HC-7213 TCGA-HC-7749 TCGA-HC-A76W TCGA-J9-A8CL TCGA-KK-A6E4 TCGA-KK-A6E5 
       40.08         1.97         7.00        13.32       115.13        49.25 
TCGA-VP-A875 TCGA-XK-AAJT TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A9WK TCGA-ZG-A9L0 
       75.91        47.15        71.77        45.86        62.37        11.67 
TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LZ 
       29.85        19.17        22.75 

$`2P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
        0.79        28.60         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        26.04        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        3.48         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
        5.85        10.62        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       40.04        41.49        30.58        41.39        36.95        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       48.72        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        53.06        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        60.99 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       10.13         4.27        37.94        36.43        22.59        20.28 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 
       12.43         3.78        16.96        19.04        12.16        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1.97              0.72 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           115.13            165.17 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           40.080            26.365 
[1] "2.0 - 115.1 (40.1)" "0.7 - 165.2 (26.4)"
[1] "hr=" "1.8"
D44V2, continuous
                   vv
clus                 T2  T3  T4
  2P LOSS MUTATED     1  13   1
  2P LOSS WILD-TYPE 187 268   9
D44V3, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T2               1               187
  T3              13               268
  T4               1                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    12   2
  2P LOSS WILD-TYPE 326  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     12    2
  2P LOSS WILD-TYPE  326   73
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              12               326
  1               2                73
[1] 2 2
[1] FALSE
D44V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  15
  2P LOSS WILD-TYPE  14 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   15
  2P LOSS WILD-TYPE   14  453
                                        clus
vv                                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 15               453
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     6   9   0   0
  2P LOSS WILD-TYPE 304 129   5  15
D44V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               6               304
  R1               9               129
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, continuous
D44V8, continuous
D44V9, continuous
D44V10, continuous
D44V11, continuous
D44V12, continuous
D44V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0     2
  2P LOSS WILD-TYPE     2                         7   144
D44V14, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               153 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7230        TCGA-HC-7231 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7750 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HI-7171 
"2P LOSS WILD-TYPE" 

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    17   1
  2Q LOSS WILD-TYPE 456   7
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               463 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                 7 
$`2Q LOSS MUTATED`
TCGA-HC-7213 TCGA-HC-7749 TCGA-HC-8266 TCGA-HC-A76W TCGA-J9-A8CL TCGA-KK-A6E4 
       40.08         1.97         1.15         7.00        13.32       115.13 
TCGA-KK-A6E5 TCGA-KK-A7B3 TCGA-KK-A8IK TCGA-VP-A875 TCGA-XK-AAJT TCGA-YL-A8HO 
       49.25        29.56        51.39        75.91        47.15        71.77 
TCGA-YL-A8SJ TCGA-YL-A9WK TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LZ 
       45.86        62.37        11.67        29.85        19.17        22.75 

$`2Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
        0.79        28.60         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        26.04        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
       22.32         1.58        15.88        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.45         1.25         4.41         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.62        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E6 
      115.86        30.02        54.54       165.17        67.59       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM 
       82.36        66.18       113.98        51.25        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 
       52.08        30.38        15.58        22.55         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78        16.31       111.39       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       41.39        36.95        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        51.45        48.72        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       14.04        53.36        60.99        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13         4.27        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       36.43        22.59        20.28        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             1.15              0.72 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           115.13            165.17 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           34.965            26.300 
[1] "1.1 - 115.1 (35.0)" "0.7 - 165.2 (26.3)"
[1] "hr=" "1.6"
D45V2, continuous
                   vv
clus                 T2  T3  T4
  2Q LOSS MUTATED     2  15   1
  2Q LOSS WILD-TYPE 186 266   9
D45V3, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T2               2               186
  T3              15               266
  T4               1                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    15   2
  2Q LOSS WILD-TYPE 323  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     15    2
  2Q LOSS WILD-TYPE  323   73
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              15               323
  1               2                73
[1] 2 2
[1] FALSE
D45V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  18
  2Q LOSS WILD-TYPE  14 450
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   18
  2Q LOSS WILD-TYPE   14  450
                                        clus
vv                                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 18               450
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     8  10   0   0
  2Q LOSS WILD-TYPE 302 128   5  15
D45V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               8               302
  R1              10               128
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, continuous
D45V8, continuous
D45V9, continuous
D45V10, continuous
D45V11, continuous
D45V12, continuous
D45V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0     2
  2Q LOSS WILD-TYPE     2                         7   144
D45V14, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               153 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7230        TCGA-HC-7231 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7750 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HI-7171 
"2Q LOSS WILD-TYPE" 

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED     9   0
  3P LOSS WILD-TYPE 464   8
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9               472 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                 8 
$`3P LOSS MUTATED`
TCGA-CH-5753 TCGA-G9-7523 TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-V1-A8WS TCGA-V1-A9O7 
        1.02        28.18        54.54       113.33        15.58        79.73 
TCGA-VP-A876 TCGA-YL-A8SQ TCGA-ZG-A9N3 
      109.58        62.79        11.47 

$`3P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 
       24.03         1.02        13.02        35.01        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        30.97        35.34        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       13.87         5.85        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 
       56.28        44.68        86.40       115.86        30.02       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
       67.59       115.13        49.25        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA 
       30.38        22.55         6.64        58.39         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       75.91        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH 
       46.29        32.45       114.38        71.34         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       37.94        36.43        29.85        22.59        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       12.43         3.78        16.96        19.04        12.16        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        13.48         4.34 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.02              0.72 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           113.33            165.17 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           54.540            26.365 
[1] "1.0 - 113.3 (54.5)" "0.7 - 165.2 (26.4)"
[1] "hr="     "2.6e+07"
D46V2, continuous
                   vv
clus                 T2  T3  T4
  3P LOSS MUTATED     1   8   0
  3P LOSS WILD-TYPE 187 273  10
D46V3, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T2               1               187
  T3               8               273
  T4               0                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     5   3
  3P LOSS WILD-TYPE 333  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    3
  3P LOSS WILD-TYPE  333   72
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               5               333
  1               3                72
[1] 2 2
[1] FALSE
D46V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   9
  3P LOSS WILD-TYPE  14 459
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    9
  3P LOSS WILD-TYPE   14  459
                                        clus
vv                                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  9               459
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED     4   4   0   1
  3P LOSS WILD-TYPE 306 134   5  14
D46V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               4               306
  R1               4               134
  R2               0                 5
  RX               1                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"
D46V7, continuous
D46V8, continuous
D46V9, continuous
D46V10, continuous
D46V11, continuous
D46V12, continuous
D46V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         0     1
  3P LOSS WILD-TYPE     2                         7   145
D46V14, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762        TCGA-CH-5763 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797        TCGA-FC-7708 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332        TCGA-G9-6333 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     5   0
  3Q LOSS WILD-TYPE 468   8
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5               476 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 8 
$`3Q LOSS MUTATED`
TCGA-G9-7523 TCGA-KK-A6E6 TCGA-V1-A9O7 TCGA-VP-A876 TCGA-YL-A8SQ 
       28.18       113.33        79.73       109.58        62.79 

$`3Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 
       38.96        27.91        30.97        35.34        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 
       54.54       165.17        67.59       115.13        49.25        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       58.39         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A879 
       25.78        16.31       111.39        75.91        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34         8.98        14.04        53.36        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
       10.13         4.27        11.67        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            28.18              0.72 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           113.33            165.17 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            79.73             26.17 
[1] "28.2 - 113.3 (79.7)" "0.7 - 165.2 (26.2)" 
[1] "hr="     "9600000"
D47V2, continuous
                   vv
clus                 T2  T3  T4
  3Q LOSS MUTATED     1   4   0
  3Q LOSS WILD-TYPE 187 277  10
D47V3, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T2               1               187
  T3               4               277
  T4               0                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5   0
  3Q LOSS WILD-TYPE 333  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    0
  3Q LOSS WILD-TYPE  333   75
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               5               333
  1               0                75
[1] 2 2
[1] FALSE
D47V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   5
  3Q LOSS WILD-TYPE  14 463
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    5
  3Q LOSS WILD-TYPE   14  463
                                        clus
vv                                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  5               463
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED     2   3   0   0
  3Q LOSS WILD-TYPE 308 135   5  15
D47V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               2               308
  R1               3               135
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, continuous
D47V8, continuous
D47V9, continuous
D47V10, continuous
D47V11, continuous
D47V12, continuous
D47V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         0     0
  3Q LOSS WILD-TYPE     2                         7   146
D47V14, multiclass

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    23   0
  4P LOSS WILD-TYPE 450   8
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               458 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                0                 8 
$`4P LOSS MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-EJ-A65B TCGA-FC-7961 
       11.51        35.01         1.02         2.04        23.34        15.42 
TCGA-HC-A48F TCGA-J9-A52B TCGA-KK-A59Z TCGA-KK-A6E1 TCGA-KK-A6E7 TCGA-KK-A7AQ 
       22.36        13.87        86.40        54.54        67.07        52.93 
TCGA-KK-A8IK TCGA-V1-A9O5 TCGA-V1-A9OL TCGA-XK-AAJT TCGA-YL-A8HK TCGA-YL-A8SL 
       51.39        58.39        19.36        47.15        49.02        32.45 
TCGA-YL-A9WH TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       14.04        12.43        22.75        17.98        11.47 

$`4P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
        1.02        13.02        31.00         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        21.96        23.80        21.96        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.77        28.41        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       27.12         5.85        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       56.28        44.68       115.86        30.02       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AU 
      115.13        49.25       113.33        58.19         6.44        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       30.58        41.39        36.95        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
        4.87        52.96        51.45        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       53.06        45.86        46.29       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
        8.98        53.36        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       28.34         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC 
       19.17         3.78        16.96        19.04        12.16        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.02              0.72 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            86.40            165.17 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           22.750            27.005 
[1] "1.0 - 86.4 (22.8)"  "0.7 - 165.2 (27.0)"
[1] "hr="     "2.6e+07"
D48V2, continuous
                   vv
clus                 T2  T3  T4
  4P LOSS MUTATED     4  17   2
  4P LOSS WILD-TYPE 184 264   8
D48V3, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T2               4               184
  T3              17               264
  T4               2                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    11  12
  4P LOSS WILD-TYPE 327  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11   12
  4P LOSS WILD-TYPE  327   63
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              11               327
  1              12                63
[1] 2 2
[1] FALSE
D48V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  22
  4P LOSS WILD-TYPE  13 446
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   22
  4P LOSS WILD-TYPE   13  446
                                        clus
vv                                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 22               446
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED     7  14   0   1
  4P LOSS WILD-TYPE 303 124   5  14
D48V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               7               303
  R1              14               124
  R2               0                 5
  RX               1                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"
D48V7, continuous
D48V8, continuous
D48V9, continuous
D48V10, continuous
D48V11, continuous
D48V12, continuous
D48V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       0                         0     4
  4P LOSS WILD-TYPE     2                         7   142
D48V14, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   4               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    16   0
  4Q LOSS WILD-TYPE 457   8
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16               465 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 8 
$`4Q LOSS MUTATED`
TCGA-CH-5751 TCGA-EJ-A65B TCGA-FC-7961 TCGA-G9-6499 TCGA-HC-A48F TCGA-J9-A52B 
       35.01        23.34        15.42        50.73        22.36        13.87 
TCGA-KK-A59Z TCGA-KK-A8IK TCGA-V1-A9O5 TCGA-YL-A8HK TCGA-YL-A8SL TCGA-YL-A9WH 
       86.40        51.39        58.39        49.02        32.45        14.04 
TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       20.28        12.43        22.75        17.98 

$`4Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A4JI 
        8.75         4.54         4.31         4.77        28.41        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       64.18        52.93        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
       15.88         1.15         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       11.77        13.55        27.12         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 
       11.57       113.10        56.28        44.68       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL 
       26.43        82.36        66.18       113.98        51.25        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48         4.87        52.96        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        53.06        45.86        46.29       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       62.79         8.98        53.36        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
        4.27        11.67        37.94        36.43        29.85        22.59 
TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC 
       19.17         3.78        16.96        19.04        12.16        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            12.43              0.72 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            86.40            165.17 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           23.045            26.990 
[1] "12.4 - 86.4 (23.0)" "0.7 - 165.2 (27.0)"
[1] "hr="     "9300000"
D49V2, continuous
                   vv
clus                 T2  T3  T4
  4Q LOSS MUTATED     3  11   2
  4Q LOSS WILD-TYPE 185 270   8
D49V3, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T2               3               185
  T3              11               270
  T4               2                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     8   8
  4Q LOSS WILD-TYPE 330  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8    8
  4Q LOSS WILD-TYPE  330   67
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               8               330
  1               8                67
[1] 2 2
[1] FALSE
D49V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     1  15
  4Q LOSS WILD-TYPE  13 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   15
  4Q LOSS WILD-TYPE   13  453
                                        clus
vv                                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 15               453
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED     5  10   0   0
  4Q LOSS WILD-TYPE 305 128   5  15
D49V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0               5               305
  R1              10               128
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, continuous
D49V8, continuous
D49V9, continuous
D49V10, continuous
D49V11, continuous
D49V12, continuous
D49V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       0                         0     3
  4Q LOSS WILD-TYPE     2                         7   143
D49V14, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    12   0
  5P LOSS WILD-TYPE 461   8
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12               469 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                 8 
$`5P LOSS MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5766 TCGA-HI-7168 TCGA-J9-A52B 
       32.71        11.51        35.01         1.02        78.61        13.87 
TCGA-J9-A8CL TCGA-VP-AA1N TCGA-YL-A9WL TCGA-ZG-A9L9 TCGA-ZG-A9LZ TCGA-ZG-A9ND 
       13.32        44.88        24.33        20.28        22.75        13.48 

$`5P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       13.02        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       12.00         1.02        23.01        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       18.84        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM 
       11.77        13.55        27.12         5.85        10.62        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        58.39        79.73         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        60.99        62.37        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        29.85        22.59        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       16.96        19.04        12.16        17.98        14.96        11.47 
TCGA-ZG-A9NI 
        4.34 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1.02              0.72 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            78.61            165.17 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           21.515            27.020 
[1] "1.0 - 78.6 (21.5)"  "0.7 - 165.2 (27.0)"
[1] "hr="     "9100000"
D50V2, continuous
                   vv
clus                 T2  T3  T4
  5P LOSS MUTATED     0  10   2
  5P LOSS WILD-TYPE 188 271   8
D50V3, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T2               0               188
  T3              10               271
  T4               2                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     7   4
  5P LOSS WILD-TYPE 331  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      7    4
  5P LOSS WILD-TYPE  331   71
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               7               331
  1               4                71
[1] 2 2
[1] FALSE
D50V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  12
  5P LOSS WILD-TYPE  14 456
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   12
  5P LOSS WILD-TYPE   14  456
                                        clus
vv                                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 12               456
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED     4   8   0   0
  5P LOSS WILD-TYPE 306 130   5  15
D50V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               4               306
  R1               8               130
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, continuous
D50V8, continuous
D50V9, continuous
D50V10, continuous
D50V11, continuous
D50V12, continuous
D50V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         0     3
  5P LOSS WILD-TYPE     2                         7   143
D50V14, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    22   0
  5Q LOSS WILD-TYPE 451   8
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               22               459 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                0                 8 
$`5Q LOSS MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-5507 TCGA-FC-A4JI 
       32.71        11.51        35.01         0.92        23.90        13.45 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HI-7168 TCGA-J9-A52B TCGA-KC-A7FA TCGA-KK-A8IF 
        1.15        22.36        78.61        13.87        19.66        26.43 
TCGA-KK-A8IK TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-VP-AA1N TCGA-YL-A9WI TCGA-YL-A9WL 
       51.39        22.55        58.39        44.88        53.36        24.33 
TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9N3 
       29.85        20.28        19.17        11.47 

$`5Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 
       13.02        31.00         1.02         2.04        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       30.31        27.19        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.77        28.41        15.42        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV 
       22.55        17.95        22.32         1.58        15.88         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        9.53        25.48        18.84        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C 
       14.37        20.28        11.77        13.55        27.12         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       67.43        69.27        82.36        66.18       113.98        51.25 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        15.58         6.64 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79         8.98        14.04        60.99        62.37 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LM 
        4.27        11.67        37.94        36.43        22.59        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        13.48         4.34 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.92              0.72 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            78.61            165.17 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           23.225            27.090 
[1] "0.9 - 78.6 (23.2)"  "0.7 - 165.2 (27.1)"
[1] "hr="     "2.6e+07"
D51V2, continuous
                   vv
clus                 T2  T3  T4
  5Q LOSS MUTATED     2  16   4
  5Q LOSS WILD-TYPE 186 265   6
D51V3, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T2               2               186
  T3              16               265
  T4               4                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    11  10
  5Q LOSS WILD-TYPE 327  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11   10
  5Q LOSS WILD-TYPE  327   65
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              11               327
  1              10                65
[1] 2 2
[1] FALSE
D51V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0  22
  5Q LOSS WILD-TYPE  14 446
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   22
  5Q LOSS WILD-TYPE   14  446
                                        clus
vv                                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 22               446
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    10  12   0   0
  5Q LOSS WILD-TYPE 300 126   5  15
D51V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              10               300
  R1              12               126
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, continuous
D51V8, continuous
D51V9, continuous
D51V10, continuous
D51V11, continuous
D51V12, continuous
D51V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         0     4
  5Q LOSS WILD-TYPE     2                         7   142
D51V14, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   4               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    23   0
  6P LOSS WILD-TYPE 450   8
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               23               458 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                0                 8 
$`6P LOSS MUTATED`
TCGA-2A-A8VT TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-7784 TCGA-HC-7213 
       32.71        23.90        48.53        52.27        25.68        40.08 
TCGA-HC-7821 TCGA-HC-A48F TCGA-HC-A632 TCGA-J9-A52B TCGA-J9-A8CL TCGA-KC-A7F6 
       31.43        22.36         2.01        13.87        13.32         8.65 
TCGA-KK-A8IC TCGA-V1-A8MG TCGA-VP-AA1N TCGA-YL-A8HO TCGA-YL-A8SQ TCGA-YL-A9WH 
       67.43        28.18        44.88        71.77        62.79        14.04 
TCGA-YL-A9WI TCGA-ZG-A8QW TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       53.36         3.09        29.85        19.17        12.43 

$`6P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       26.30        45.73        28.93        30.31        27.19        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        36.69        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       47.80        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.77        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       28.54         0.79        28.60         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 
       25.71        30.51        30.84        17.85        24.56        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV 
       17.95        22.32         1.58        15.88         1.15         0.76 
TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        1.78         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C 
       14.37        20.28        11.77        13.55        27.12         5.85 
TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.62        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FA TCGA-KC-A7FD 
       19.96        44.35        43.66        21.86        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48         2.73        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       13.32        41.23        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       71.34         8.98        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
       28.34        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9LS 
       37.94        36.43        22.59        20.28         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             2.01              0.72 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            71.77            165.17 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           28.180            26.545 
[1] "2.0 - 71.8 (28.2)"  "0.7 - 165.2 (26.5)"
[1] "hr="     "2.6e+07"
D52V2, continuous
                   vv
clus                 T2  T3  T4
  6P LOSS MUTATED     3  17   3
  6P LOSS WILD-TYPE 185 264   7
D52V3, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T2               3               185
  T3              17               264
  T4               3                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    12   9
  6P LOSS WILD-TYPE 326  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     12    9
  6P LOSS WILD-TYPE  326   66
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              12               326
  1               9                66
[1] 2 2
[1] FALSE
D52V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0  23
  6P LOSS WILD-TYPE  14 445
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   23
  6P LOSS WILD-TYPE   14  445
                                        clus
vv                                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 23               445
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    10  12   0   0
  6P LOSS WILD-TYPE 300 126   5  15
D52V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              10               300
  R1              12               126
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, continuous
D52V8, continuous
D52V9, continuous
D52V10, continuous
D52V11, continuous
D52V12, continuous
D52V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       0                         1     5
  6P LOSS WILD-TYPE     2                         6   141
D52V14, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   5               141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    36   1
  6Q LOSS WILD-TYPE 437   7
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               37               444 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                 7 
$`6Q LOSS MUTATED`
TCGA-2A-A8VT TCGA-CH-5753 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-7782 
       32.71         1.02        23.90        48.53        52.27        38.37 
TCGA-EJ-7784 TCGA-EJ-7786 TCGA-FC-7961 TCGA-G9-A9S0 TCGA-HC-7078 TCGA-HC-7213 
       25.68        14.53        15.42        26.01        65.26        40.08 
TCGA-HC-7821 TCGA-HC-A48F TCGA-HC-A632 TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CL 
       31.43        22.36         2.01        13.87        10.62        13.32 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KK-A6E1 TCGA-KK-A8IC TCGA-VN-A88O TCGA-VP-AA1N 
        8.65        19.66        54.54        67.43        15.81        44.88 
TCGA-X4-A8KQ TCGA-XJ-A9DI TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8SQ TCGA-YL-A9WH 
       45.47        48.03        37.25        71.77        62.79        14.04 
TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       53.36        62.37         3.09        29.85        19.17        12.43 
TCGA-ZG-A9ND 
       13.48 

$`6Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        35.01        31.00         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 
       45.73        28.93        30.31        27.19        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7788 
        6.28        24.39        23.90        25.87        20.55        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A4JI 
        8.75         4.54         4.31         4.77        28.41        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       35.34        28.18        32.68        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
        3.68        19.76         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       28.54         0.79        28.60         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 
       25.71        30.51        30.84        17.85        24.56        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV 
       17.95        22.32         1.58        15.88         1.15         0.76 
TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        1.78         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C 
       14.37        20.28        11.77        13.55        27.12         5.85 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       44.35        43.66        21.86         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 
       56.28        44.68        86.40       115.86        30.02       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
       63.48         2.73        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       30.38        15.58        22.55         6.64        58.39        79.73 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
        6.71        20.91        38.93        41.19        19.36        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87         4.70         5.82         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
        6.21        15.52        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       14.76        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        31.99        31.96        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       71.34         8.98        60.99        24.33        49.91        28.34 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       36.43        22.59        20.28         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       12.16        22.75        17.98        14.96        11.47         4.34 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1.02              0.72 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            71.77            165.17 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           26.010            26.825 
[1] "1.0 - 71.8 (26.0)"  "0.7 - 165.2 (26.8)"
[1] "hr=" "2.2"
D53V2, continuous
                   vv
clus                 T2  T3  T4
  6Q LOSS MUTATED     6  28   3
  6Q LOSS WILD-TYPE 182 253   7
D53V3, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T2               6               182
  T3              28               253
  T4               3                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    23  13
  6Q LOSS WILD-TYPE 315  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     23   13
  6Q LOSS WILD-TYPE  315   62
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              23               315
  1              13                62
[1] 2 2
[1] FALSE
D53V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0  37
  6Q LOSS WILD-TYPE  14 431
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   37
  6Q LOSS WILD-TYPE   14  431
                                        clus
vv                                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 37               431
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    18  15   0   2
  6Q LOSS WILD-TYPE 292 123   5  13
D53V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              18               292
  R1              15               123
  R2               0                 5
  RX               2                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, continuous
D53V8, continuous
D53V9, continuous
D53V10, continuous
D53V11, continuous
D53V12, continuous
D53V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       0                         2     9
  6Q LOSS WILD-TYPE     2                         5   137
D53V14, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                   9               137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 8P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   158   3
  8P LOSS WILD-TYPE 315   5
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              161               320 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                 5 
$`8P LOSS MUTATED`
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYO 
       32.71        22.06        33.96         3.68        25.35        30.31 
TCGA-2A-AAYU TCGA-CH-5739 TCGA-CH-5744 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5764 
       20.22        22.06         1.97         1.02         2.04         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5790 
       23.01         1.02        15.06        13.02        26.99        32.02 
TCGA-CH-5791 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 
       33.01        46.52        44.88        23.90        48.53        52.27 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7314 
       39.75        60.23        47.87        29.06        88.34        37.81 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7788 
       27.09        35.18         6.28        23.90        25.87        14.14 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A65D TCGA-EJ-A65E 
       76.41        38.10        24.85        25.18        12.92        13.71 
TCGA-EJ-A8FS TCGA-FC-7708 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6339 TCGA-G9-6342 
        8.75        28.41        87.35        81.04        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6364 TCGA-G9-6369 TCGA-G9-6371 
       18.21        49.35        46.52        39.39        39.95        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-7509 
       26.66        31.50        25.15        58.22        56.75        52.93 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7744 
       26.01        23.93         6.08        40.08         2.37         1.68 
TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8262 
       17.85        31.43        22.42        28.27        23.87        22.32 
TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AQ 
        1.58        22.36         2.01         2.20         1.61         3.48 
TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67S 
       78.61        82.92        43.69        30.94        16.54        27.39 
TCGA-J4-A83I TCGA-J4-A83N TCGA-J4-AATZ TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN 
       22.52        20.28        13.55        10.62        13.32        40.67 
TCGA-KC-A4BV TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KK-A59Y TCGA-KK-A6E1 TCGA-KK-A6E5 
       43.66         8.65         8.88        44.68        54.54        49.25 
TCGA-KK-A7AP TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B4 TCGA-KK-A8I5 
        6.44        27.02        34.65        49.94        20.94       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8II 
       21.96        32.91        63.48        26.43        82.36       113.98 
TCGA-KK-A8IM TCGA-M7-A71Z TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IO TCGA-SU-A7E7 
       47.28        21.14        18.84         5.69       122.17        18.12 
TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8WL TCGA-V1-A8WS TCGA-V1-A8X3 
       13.32        28.18        40.44        52.08        15.58         6.64 
TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OL TCGA-VN-A88K TCGA-VN-A88O 
       79.73        20.91        41.19        19.36        25.51        15.81 
TCGA-VN-A88P TCGA-VN-A88R TCGA-VP-A875 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87J 
       41.42        25.78        75.91        85.18        55.56        53.36 
TCGA-VP-A87K TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DQ TCGA-XK-AAIR 
       42.94        37.05        38.04        42.08         2.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-YJ-A8SW TCGA-YL-A8HK 
       37.25        41.49        41.39        36.95         4.87        49.02 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SR 
       41.46        45.14        45.86        32.45        71.34         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A9L0 TCGA-ZG-A9LS 
       14.04        53.36        24.33        49.91        11.67        16.96 
TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        17.98        14.96        13.48         4.34 

$`8P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-AAYF TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       20.42        43.79        31.96        11.51         2.99         6.97 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
        1.02        12.99        13.97        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5768 
       35.01        31.00         0.92        44.02        12.00        24.03 
TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        2.04        15.98         9.99         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5502 TCGA-EJ-5503 
       33.11        19.56        13.32        29.79        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       28.93        30.31        27.19        38.93        48.13        36.69 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 
       38.53        36.23        60.23        46.55        47.80        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5531 
       51.88        68.35        43.07        36.66        38.76        41.85 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 
       74.10        93.70        83.57        36.13        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 
       33.83        30.35        27.68        24.39        38.37        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        14.53        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       23.05        19.92        77.16        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65F 
       25.74        21.96        23.80        21.96        23.34        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7961 
        9.27         9.83         4.54         4.31         4.77        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       67.99        66.67        68.68        49.81        46.16        50.70 
TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.15        47.44        45.30        44.81         3.32        40.18 
TCGA-G9-6370 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6498 TCGA-G9-6499 
       38.01        37.97        58.45        27.29        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
       37.35        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.48        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8258 
       25.71        30.51        30.84        24.56        19.36         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV 
        2.27        22.55        17.95        15.88         1.15         0.76 
TCGA-HC-A631 TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.78        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        7.00         4.93         9.53        25.48        18.84        88.24 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67O TCGA-J4-A67Q 
       20.19        12.30        33.01        25.32        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J 
       29.92         6.02        25.28        27.91        16.83        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B 
       10.78        23.67        14.37        11.77        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
        5.85        15.22        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7FA TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       44.35        21.86        19.66        11.57       113.10        56.28 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       86.40       115.86        30.02       165.17        67.59       115.13 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AY 
      113.33        67.07        58.19        52.93        58.36        51.68 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I7 
       32.84        34.95        36.13        29.56        67.99        65.82 
TCGA-KK-A8I8 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8IJ 
       31.79         2.73        67.43        69.27        66.18        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       51.39        20.65         5.19        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP 
       25.08        29.23         3.19        41.00       140.19        86.14 
TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       11.90        41.23        16.70        14.73        39.29        53.16 
TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OQ 
       30.38        22.55        58.39         6.71        38.93        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M 
       49.87         4.70         5.82         8.84        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 
       15.52        44.91        16.31       111.39       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-AA1N TCGA-WW-A8ZI 
       23.93        60.92        66.97        21.80        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DX 
       45.47        32.19         3.91        48.03         9.04        31.99 
TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       40.04        30.58        47.15        51.81        32.19        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO 
       16.83        56.52        28.77        53.06        46.29       114.38 
TCGA-YL-A8SQ TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.79        60.99        62.37        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
       13.28        10.13         4.27        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LU 
       22.59        20.28        19.17        12.43         3.78        19.04 
TCGA-ZG-A9LZ TCGA-ZG-A9N3 
       22.75        11.47 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1.02              0.72 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           122.17            165.17 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           27.390            25.695 
[1] "1.0 - 122.2 (27.4)" "0.7 - 165.2 (25.7)"
[1] "hr=" "1.3"
D54V2, continuous
                   vv
clus                 T2  T3  T4
  8P LOSS MUTATED    44 115   3
  8P LOSS WILD-TYPE 144 166   7
D54V3, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T2              44               144
  T3             115               166
  T4               3                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   110  31
  8P LOSS WILD-TYPE 228  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    110   31
  8P LOSS WILD-TYPE  228   44
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             110               228
  1              31                44
[1] 2 2
[1] FALSE
D54V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     5 157
  8P LOSS WILD-TYPE   9 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5  157
  8P LOSS WILD-TYPE    9  311
                                        clus
vv                                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               5                 9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                157               311
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   102  46   2   8
  8P LOSS WILD-TYPE 208  92   3   7
D54V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             102               208
  R1              46                92
  R2               2                 3
  RX               8                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, continuous
D54V8, continuous
D54V9, continuous
D54V10, continuous
D54V11, continuous
D54V12, continuous
D54V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       2                         3    47
  8P LOSS WILD-TYPE     0                         4    99
D54V14, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   2                 0
  BLACK OR AFRICAN AMERICAN               3                 4
  WHITE                                  47                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 8Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    21   2
  8Q LOSS WILD-TYPE 452   6
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               23               458 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                 6 
$`8Q LOSS MUTATED`
TCGA-2A-A8VT TCGA-CH-5739 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5764 TCGA-EJ-5507 
       32.71        22.06         1.02         2.04         1.02        23.90 
TCGA-EJ-5527 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-A9S0 TCGA-HC-7744 TCGA-HI-7168 
       39.75        58.22        52.93        26.01         1.68        78.61 
TCGA-HI-7171 TCGA-J9-A52E TCGA-KK-A59Y TCGA-KK-A8IF TCGA-MG-AAMC TCGA-TP-A8TV 
       43.69        10.62        44.68        26.43         5.69        13.32 
TCGA-V1-A8WL TCGA-V1-A8WS TCGA-YL-A8SF TCGA-YL-A9WH TCGA-YL-A9WI 
       52.08        15.58        45.14        14.04        53.36 

$`8Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         2.99         6.97 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       13.02        35.01        31.00         0.92        44.02        12.00 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       27.19        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 
       51.88        68.35        43.07        36.66        38.76        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        64.18        50.73        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       35.34        28.18        32.68        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
       23.57         1.48        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       88.24        82.92        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       27.12        13.87         5.85        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       56.28        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH 
       63.48         2.73        67.43        69.27        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       18.12        11.90        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8X3 
       14.73        39.29        53.16        30.38        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK 
      114.38        71.34        62.79         8.98        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
       10.13         4.27        11.67        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.02              0.72 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            78.61            165.17 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           26.010            27.005 
[1] "1.0 - 78.6 (26.0)"  "0.7 - 165.2 (27.0)"
[1] "hr=" "11" 
D55V2, continuous
                   vv
clus                 T2  T3  T4
  8Q LOSS MUTATED     2  19   2
  8Q LOSS WILD-TYPE 186 262   8
D55V3, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T2               2               186
  T3              19               262
  T4               2                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    13   8
  8Q LOSS WILD-TYPE 325  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     13    8
  8Q LOSS WILD-TYPE  325   67
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              13               325
  1               8                67
[1] 2 2
[1] FALSE
D55V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  23
  8Q LOSS WILD-TYPE  14 445
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   23
  8Q LOSS WILD-TYPE   14  445
                                        clus
vv                                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 23               445
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    12  10   0   1
  8Q LOSS WILD-TYPE 298 128   5  14
D55V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              12               298
  R1              10               128
  R2               0                 5
  RX               1                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"
D55V7, continuous
D55V8, continuous
D55V9, continuous
D55V10, continuous
D55V11, continuous
D55V12, continuous
D55V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         0    10
  8Q LOSS WILD-TYPE     2                         7   136
D55V14, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  10               136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 9P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    20   0
  9P LOSS WILD-TYPE 453   8
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               20               461 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                0                 8 
$`9P LOSS MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-EJ-5507 TCGA-EJ-5521 TCGA-EJ-7781 TCGA-FC-7961 
       11.51        35.01        23.90        51.88        23.90        15.42 
TCGA-G9-7521 TCGA-HC-8216 TCGA-HC-A631 TCGA-HI-7168 TCGA-J4-A67L TCGA-J9-A52E 
       30.97        22.42         1.78        78.61        25.32        10.62 
TCGA-KC-A7F6 TCGA-KK-A6DY TCGA-KK-A8IB TCGA-KK-A8IC TCGA-V1-A8WS TCGA-V1-A9O5 
        8.65       115.86         2.73        67.43        15.58        58.39 
TCGA-VP-A87D TCGA-YL-A9WY 
       60.92        28.34 

$`9P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 
       45.73        28.93        30.31        27.19        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       47.80        52.27        64.50        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
       27.68         6.28        24.39        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.77        28.41        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       38.96        27.91        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       12.30        33.01        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CL 
       11.77        13.55        27.12        13.87         5.85        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       44.35        43.66        21.86        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        56.28        44.68        86.40        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
       32.91        63.48        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       30.38        22.55         6.64        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        62.37        24.33        49.91 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       37.94        36.43        29.85        22.59        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       12.43         3.78        16.96        19.04        12.16        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.78              0.72 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           115.86            165.17 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            24.61             26.99 
[1] "1.8 - 115.9 (24.6)" "0.7 - 165.2 (27.0)"
[1] "hr="     "8.1e+07"
D56V2, continuous
                   vv
clus                 T2  T3  T4
  9P LOSS MUTATED     4  14   2
  9P LOSS WILD-TYPE 184 267   8
D56V3, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T2               4               184
  T3              14               267
  T4               2                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    13   6
  9P LOSS WILD-TYPE 325  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     13    6
  9P LOSS WILD-TYPE  325   69
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              13               325
  1               6                69
[1] 2 2
[1] FALSE
D56V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     0  20
  9P LOSS WILD-TYPE  14 448
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   20
  9P LOSS WILD-TYPE   14  448
                                        clus
vv                                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 20               448
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    12   7   0   0
  9P LOSS WILD-TYPE 298 131   5  15
D56V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              12               298
  R1               7               131
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, continuous
D56V8, continuous
D56V9, continuous
D56V10, continuous
D56V11, continuous
D56V12, continuous
D56V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       0                         0     6
  9P LOSS WILD-TYPE     2                         7   140
D56V14, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   6               140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = 9Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED     9   0
  9Q LOSS WILD-TYPE 464   8
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                9               472 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                0                 8 
$`9Q LOSS MUTATED`
TCGA-4L-AA1F TCGA-EJ-5514 TCGA-EJ-7781 TCGA-FC-7961 TCGA-HI-7168 TCGA-J9-A52E 
       11.51        36.23        23.90        15.42        78.61        10.62 
TCGA-V1-A8WS TCGA-V1-A9O5 TCGA-YL-A9WY 
       15.58        58.39        28.34 

$`9Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 
       38.93        48.13        36.69        48.53        38.53        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       35.18        30.35        27.68         6.28        24.39        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.54         4.31         4.77        28.41        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       18.84        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CL 
       11.77        13.55        27.12        13.87         5.85        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WV 
       14.73        39.29        53.16        52.08        30.38        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW 
       53.36        60.99        62.37        24.33        49.91         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            10.62              0.72 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            78.61            165.17 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           23.900            26.825 
[1] "10.6 - 78.6 (23.9)" "0.7 - 165.2 (26.8)"
[1] "hr="     "9100000"
D57V2, continuous
                   vv
clus                 T2  T3  T4
  9Q LOSS MUTATED     2   6   1
  9Q LOSS WILD-TYPE 186 275   9
D57V3, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T2               2               186
  T3               6               275
  T4               1                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     6   2
  9Q LOSS WILD-TYPE 332  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6    2
  9Q LOSS WILD-TYPE  332   73
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               6               332
  1               2                73
[1] 2 2
[1] FALSE
D57V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     0   9
  9Q LOSS WILD-TYPE  14 459
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0    9
  9Q LOSS WILD-TYPE   14  459
                                        clus
vv                                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  9               459
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED     4   4   0   0
  9Q LOSS WILD-TYPE 306 134   5  15
D57V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0               4               306
  R1               4               134
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, continuous
D57V8, continuous
D57V9, continuous
D57V10, continuous
D57V11, continuous
D57V12, continuous
D57V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       0                         0     4
  9Q LOSS WILD-TYPE     2                         7   142
D57V14, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   4               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = 10P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    39   1
  10P LOSS WILD-TYPE 434   7
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                40                441 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                  7 
$`10P LOSS MUTATED`
TCGA-2A-A8VT TCGA-CH-5751 TCGA-CH-5788 TCGA-CH-5790 TCGA-EJ-5518 TCGA-EJ-7784 
       32.71        35.01        26.99        32.02        52.27        25.68 
TCGA-FC-7961 TCGA-G9-6363 TCGA-G9-6377 TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-7232 
       15.42        45.30        31.50        30.97        40.08        38.17 
TCGA-HC-A48F TCGA-HI-7168 TCGA-HI-7171 TCGA-J9-A52B TCGA-J9-A8CP TCGA-KK-A59Z 
       22.36        78.61        43.69        13.87        12.69        86.40 
TCGA-KK-A6E6 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-M7-A721 TCGA-V1-A9O5 TCGA-V1-A9Z7 
      113.33        20.94       101.79        13.15        58.39         4.27 
TCGA-VP-A875 TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-XK-AAIV TCGA-XK-AAJ3 
       75.91        53.36        42.94        44.88        37.25        41.49 
TCGA-XK-AAJT TCGA-YL-A8HL TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WK 
       47.15        51.45        45.86        32.45        62.79        62.37 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L9 TCGA-ZG-A9LS 
        4.27        11.67        20.28        16.96 

$`10P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5791 
       24.03         2.04        13.02        15.98         9.99        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
        6.28        24.39        23.90        38.37        25.87        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6364 TCGA-G9-6365 
       49.35        47.15        46.52        47.44        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 
       64.18        50.73        52.93        38.96        27.91        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54         0.79        28.60         1.68         2.37 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 
        4.93         9.53        25.48        18.84        88.24        82.92 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C 
       14.37        20.28        11.77        13.55        27.12         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-KC-A4BL TCGA-KC-A4BN 
       10.62        13.32        15.22        40.67        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY 
        8.88        11.57       113.10        56.28        44.68       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       29.56        67.99        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        5.19        21.14        12.62        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 
       30.38        15.58        22.55         6.64        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        8.42         5.59         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       66.97        21.80        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.99        31.96        40.04        30.58        41.39        36.95 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO 
       41.46        45.14        28.77        53.06        46.29       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL 
       71.34         8.98        14.04        53.36        60.99        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         3.09        14.53        13.28        10.13 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       37.94        36.43        29.85        22.59        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
        3.78        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              4.27               0.72 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            113.33             165.17 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             37.71              25.71 
[1] "4.3 - 113.3 (37.7)" "0.7 - 165.2 (25.7)"
[1] "hr=" "1.5"
D58V2, continuous
                    vv
clus                  T2  T3  T4
  10P LOSS MUTATED     7  27   6
  10P LOSS WILD-TYPE 181 254   4
D58V3, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T2                7                181
  T3               27                254
  T4                6                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    22  15
  10P LOSS WILD-TYPE 316  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     22   15
  10P LOSS WILD-TYPE  316   60
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               22                316
  1               15                 60
[1] 2 2
[1] FALSE
D58V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  39
  10P LOSS WILD-TYPE  13 429
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   39
  10P LOSS WILD-TYPE   13  429
                                        clus
vv                                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  39                429
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    18  20   1   0
  10P LOSS WILD-TYPE 292 118   4  15
D58V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               18                292
  R1               20                118
  R2                1                  4
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, continuous
D58V8, continuous
D58V9, continuous
D58V10, continuous
D58V11, continuous
D58V12, continuous
D58V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         0    12
  10P LOSS WILD-TYPE     2                         7   134
D58V14, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   12                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 10Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    40   1
  10Q LOSS WILD-TYPE 433   7
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                41                440 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                  7 
$`10Q LOSS MUTATED`
TCGA-2A-A8VT TCGA-CH-5751 TCGA-CH-5790 TCGA-EJ-5507 TCGA-EJ-5518 TCGA-EJ-7784 
       32.71        35.01        32.02        23.90        52.27        25.68 
TCGA-FC-7961 TCGA-G9-6348 TCGA-G9-6377 TCGA-G9-6499 TCGA-G9-7521 TCGA-HC-7213 
       15.42        49.81        31.50        50.73        30.97        40.08 
TCGA-HC-7232 TCGA-HC-7737 TCGA-HC-8266 TCGA-HC-A48F TCGA-HI-7168 TCGA-HI-7171 
       38.17         2.10         1.15        22.36        78.61        43.69 
TCGA-J9-A52B TCGA-KK-A59Z TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7B4 TCGA-KK-A8I5 
       13.87        86.40       113.33        67.07        20.94       101.79 
TCGA-M7-A721 TCGA-V1-A9O5 TCGA-V1-A9Z7 TCGA-VP-A875 TCGA-VP-A87K TCGA-VP-AA1N 
       13.15        58.39         4.27        75.91        42.94        44.88 
TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YL-A8HL TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SL 
       37.25        47.15        51.45        45.14        45.86        32.45 
TCGA-YL-A9WK TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L9 TCGA-ZG-A9M4 
       62.37         4.27        11.67        20.28        17.98 

$`10Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       28.93        30.31        27.19        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
        6.28        24.39        23.90        38.37        25.87        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       55.76        18.21        68.68        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       64.18        52.93        38.96        27.91        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 
       28.54         0.79        28.60         1.68         2.37        44.55 
TCGA-HC-7736 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        0.72        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       22.32         1.58        15.88         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       18.84        88.24        82.92        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       13.55        27.12         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        56.28        44.68       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AP 
      165.17        67.59       115.13        49.25        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I6 
       32.84        34.95        36.13        29.56        67.99        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 
       19.36        12.20        15.65         8.42         5.59         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78        16.31       111.39       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       40.04        41.49        30.58        41.39        36.95        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HM 
       32.19        25.48         4.87        52.96        49.02        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       28.77        53.06        46.29       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
        8.98        14.04        53.36        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L2 
       28.34         3.09        14.53        13.28        10.13        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        29.85        22.59        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 
       16.96        19.04        12.16        22.75        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1.15               0.72 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            113.33             165.17 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             37.25              25.76 
[1] "1.1 - 113.3 (37.2)" "0.7 - 165.2 (25.8)"
[1] "hr=" "1.5"
D59V2, continuous
                    vv
clus                  T2  T3  T4
  10Q LOSS MUTATED     9  27   5
  10Q LOSS WILD-TYPE 179 254   5
D59V3, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T2                9                179
  T3               27                254
  T4                5                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    23  16
  10Q LOSS WILD-TYPE 315  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     23   16
  10Q LOSS WILD-TYPE  315   59
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               23                315
  1               16                 59
[1] 2 2
[1] FALSE
D59V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  40
  10Q LOSS WILD-TYPE  13 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   40
  10Q LOSS WILD-TYPE   13  428
                                        clus
vv                                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  40                428
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    18  22   0   0
  10Q LOSS WILD-TYPE 292 116   5  15
D59V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               18                292
  R1               22                116
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, continuous
D59V8, continuous
D59V9, continuous
D59V10, continuous
D59V11, continuous
D59V12, continuous
D59V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       0                         1    13
  10Q LOSS WILD-TYPE     2                         6   133
D59V14, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   13                133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 11P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     7   0
  11P LOSS WILD-TYPE 466   8
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                474 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 0                  8 
$`11P LOSS MUTATED`
TCGA-EJ-8472 TCGA-G9-6379 TCGA-J9-A8CL TCGA-KK-A8IK TCGA-V1-A8MG TCGA-VP-AA1N 
       24.85        58.45        13.32        51.39        28.18        44.88 
TCGA-ZG-A9KY 
        4.27 

$`11P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        77.16        76.41        38.10        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       26.66        31.50        37.97        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
       13.87         5.85        10.62        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18       113.98        51.25        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ 
       86.14        18.12        11.90        13.32        41.23        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       37.25        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         3.09        14.53        13.28        10.13 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              4.27               0.72 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             58.45             165.17 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            28.180             26.545 
[1] "4.3 - 58.5 (28.2)"  "0.7 - 165.2 (26.5)"
[1] "hr="     "9200000"
D60V2, continuous
                    vv
clus                  T2  T3  T4
  11P LOSS MUTATED     1   5   1
  11P LOSS WILD-TYPE 187 276   9
D60V3, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T2                1                187
  T3                5                276
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4   1
  11P LOSS WILD-TYPE 334  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    1
  11P LOSS WILD-TYPE  334   74
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                4                334
  1                1                 74
[1] 2 2
[1] FALSE
D60V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0   7
  11P LOSS WILD-TYPE  14 461
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    7
  11P LOSS WILD-TYPE   14  461
                                        clus
vv                                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   7                461
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED     2   5   0   0
  11P LOSS WILD-TYPE 308 133   5  15
D60V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                2                308
  R1                5                133
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, continuous
D60V8, continuous
D60V9, continuous
D60V10, continuous
D60V11, continuous
D60V12, continuous
D60V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       0                         0     0
  11P LOSS WILD-TYPE     2                         7   146
D60V14, multiclass

Clustering(61) Variable = 11Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED     5   0
  11Q LOSS WILD-TYPE 468   8
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                476 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 0                  8 
$`11Q LOSS MUTATED`
TCGA-J9-A52C TCGA-J9-A8CL TCGA-V1-A8MG TCGA-ZG-A9KY TCGA-ZG-A9NI 
        5.85        13.32        28.18         4.27         4.34 

$`11Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN 
       13.55        27.12        13.87        10.62        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       41.23        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 
       52.08        30.38        15.58        22.55         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       11.47        13.48 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              4.27               0.72 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             28.18             165.17 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             5.850             27.005 
[1] "4.3 - 28.2 (5.8)"   "0.7 - 165.2 (27.0)"
[1] "hr="     "1200000"
D61V2, continuous
                    vv
clus                  T2  T3  T4
  11Q LOSS MUTATED     0   4   1
  11Q LOSS WILD-TYPE 188 277   9
D61V3, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T2                0                188
  T3                4                277
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1   1
  11Q LOSS WILD-TYPE 337  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1    1
  11Q LOSS WILD-TYPE  337   74
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                1                337
  1                1                 74
[1] 2 2
[1] FALSE
D61V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0   5
  11Q LOSS WILD-TYPE  14 463
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    5
  11Q LOSS WILD-TYPE   14  463
                                        clus
vv                                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   5                463
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED     1   4   0   0
  11Q LOSS WILD-TYPE 309 134   5  15
D61V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                1                309
  R1                4                134
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                393 
        TCGA-2A-A8VL         TCGA-2A-A8VT         TCGA-2A-A8VV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-2A-A8VX         TCGA-2A-A8W1         TCGA-2A-A8W3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-2A-AAYU         TCGA-4L-AA1F         TCGA-CH-5737 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5739         TCGA-CH-5740         TCGA-CH-5741 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5743         TCGA-CH-5744         TCGA-CH-5746 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5748         TCGA-CH-5750         TCGA-CH-5751 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5752         TCGA-CH-5753         TCGA-CH-5754 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5761         TCGA-CH-5762         TCGA-CH-5763 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5764         TCGA-CH-5765         TCGA-CH-5766 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5772         TCGA-CH-5788 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5789         TCGA-CH-5790         TCGA-CH-5791 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5502         TCGA-EJ-5503         TCGA-EJ-5504 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5506         TCGA-EJ-5507 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7218         TCGA-EJ-7312         TCGA-EJ-7314 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7321 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7325         TCGA-EJ-7327         TCGA-EJ-7328 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7794         TCGA-EJ-7797         TCGA-EJ-8468 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-8469         TCGA-EJ-8470         TCGA-EJ-8472 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-8474         TCGA-EJ-A46B         TCGA-EJ-A46D 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A46E         TCGA-EJ-A46F         TCGA-EJ-A46G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A65B         TCGA-EJ-A65D         TCGA-EJ-A65E 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A65F         TCGA-EJ-A65G         TCGA-EJ-A65J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A65M         TCGA-EJ-A6RA         TCGA-EJ-A6RC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A7NF         TCGA-EJ-A7NG         TCGA-EJ-A7NJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A7NK         TCGA-EJ-A7NM         TCGA-EJ-A8FN 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A8FO         TCGA-EJ-A8FP         TCGA-EJ-A8FS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A8FU         TCGA-EJ-AB20         TCGA-EJ-AB27 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-FC-A5OB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FC-A66V         TCGA-FC-A6HD         TCGA-FC-A8O0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6339         TCGA-G9-6348 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6367         TCGA-G9-6369         TCGA-G9-6370 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6379         TCGA-G9-6384 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6494         TCGA-G9-6496         TCGA-G9-6499 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-7510         TCGA-G9-7521         TCGA-G9-7522 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-7523         TCGA-G9-7525         TCGA-G9-A9S0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-A9S7         TCGA-H9-A6BY         TCGA-HC-7078 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7079         TCGA-HC-7080         TCGA-HC-7209 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7233 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7736         TCGA-HC-7737         TCGA-HC-7740 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7821         TCGA-HC-8216         TCGA-HC-8257 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-8258         TCGA-HC-8260         TCGA-HC-8262 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-8264         TCGA-HC-8265         TCGA-HC-8266 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-A48F         TCGA-HC-A4ZV         TCGA-HC-A631 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-A632         TCGA-HC-A6AL         TCGA-HC-A6AN 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-A6AS         TCGA-HC-A6HX         TCGA-HC-A76W 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-A76X         TCGA-HC-A8CY         TCGA-HC-A8D0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-A8D1         TCGA-HI-7168         TCGA-HI-7169 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HI-7170         TCGA-HI-7171         TCGA-J4-8200 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-J4-A67L         TCGA-J4-A67M         TCGA-J4-A67N 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-J4-A67O         TCGA-J4-A67R         TCGA-J4-A67S 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-J4-A6G1         TCGA-J4-A6G3         TCGA-J4-A83I 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-J4-A83J         TCGA-J4-A83L         TCGA-J4-A83M 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-J4-AATZ         TCGA-J4-AAU2         TCGA-J9-A52B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-J9-A52E         TCGA-J9-A8CM         TCGA-KC-A4BL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KC-A4BN         TCGA-KC-A4BO         TCGA-KC-A4BR 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KC-A4BV         TCGA-KC-A7F3         TCGA-KC-A7F6 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KC-A7FA         TCGA-KC-A7FD         TCGA-KC-A7FE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A59V         TCGA-KK-A59X         TCGA-KK-A59Y 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A59Z         TCGA-KK-A6DY         TCGA-KK-A6E0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A6E1         TCGA-KK-A6E2         TCGA-KK-A6E3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A6E4         TCGA-KK-A6E5         TCGA-KK-A6E6 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A6E7         TCGA-KK-A6E8         TCGA-KK-A7AP 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A7AQ         TCGA-KK-A7AU         TCGA-KK-A7AV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A7AW         TCGA-KK-A7AY         TCGA-KK-A7AZ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A7B0         TCGA-KK-A7B1         TCGA-KK-A7B2 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A7B3         TCGA-KK-A7B4         TCGA-KK-A8I4 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A8I6         TCGA-KK-A8I7         TCGA-KK-A8IA 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A8ID         TCGA-KK-A8IJ         TCGA-KK-A8IL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-M7-A71Z         TCGA-M7-A722         TCGA-M7-A723 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-M7-A724         TCGA-M7-A725         TCGA-QU-A6IL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-QU-A6IM         TCGA-QU-A6IN         TCGA-QU-A6IO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-QU-A6IP         TCGA-SU-A7E7         TCGA-TP-A8TT 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-TP-A8TV         TCGA-V1-A8MF         TCGA-V1-A8MJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A8ML         TCGA-V1-A8MM         TCGA-V1-A8MU 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A8WL         TCGA-V1-A8WV         TCGA-V1-A8X3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A9O5         TCGA-V1-A9O7         TCGA-V1-A9O9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A9OA         TCGA-V1-A9OL         TCGA-V1-A9OX 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A9OY         TCGA-V1-A9Z7         TCGA-V1-A9Z8 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A9Z9         TCGA-V1-A9ZG         TCGA-V1-A9ZI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-VN-A88I         TCGA-VN-A88K         TCGA-VN-A88L 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-VN-A88M         TCGA-VN-A88N         TCGA-VN-A88O 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-VN-A88P         TCGA-VN-A88Q         TCGA-VN-A88R 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-VN-A943         TCGA-VP-A872         TCGA-VP-A875 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-VP-A876         TCGA-VP-A878         TCGA-VP-A879 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-VP-A87B         TCGA-VP-A87C         TCGA-VP-A87D 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-VP-A87E         TCGA-VP-A87H         TCGA-VP-A87J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-VP-A87K         TCGA-VP-AA1N         TCGA-WW-A8ZI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-X4-A8KQ         TCGA-XA-A8JR         TCGA-XJ-A83F 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-XJ-A83G         TCGA-XJ-A9DI         TCGA-XJ-A9DX 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-XK-AAIR         TCGA-XK-AAIV         TCGA-XK-AAIW 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-XK-AAJ3         TCGA-XK-AAJA         TCGA-XK-AAJP 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-XK-AAJR         TCGA-XK-AAJT         TCGA-XK-AAJU 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-XK-AAK1         TCGA-Y6-A8TL         TCGA-YJ-A8SW 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-YL-A8HK         TCGA-YL-A8HL         TCGA-YL-A8HM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-YL-A8HO         TCGA-YL-A8S8         TCGA-YL-A8S9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-YL-A8SA         TCGA-YL-A8SB         TCGA-YL-A8SC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-YL-A8SF         TCGA-YL-A8SH         TCGA-YL-A8SI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-YL-A8SJ         TCGA-YL-A8SK         TCGA-YL-A8SL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-YL-A8SQ         TCGA-YL-A8SR         TCGA-YL-A9WH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-YL-A9WI         TCGA-YL-A9WJ         TCGA-YL-A9WK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-YL-A9WL         TCGA-YL-A9WX         TCGA-YL-A9WY 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A8QW         TCGA-ZG-A8QX         TCGA-ZG-A8QY 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A8QZ         TCGA-ZG-A9L0         TCGA-ZG-A9L2 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9L4         TCGA-ZG-A9L5         TCGA-ZG-A9L6 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9L9         TCGA-ZG-A9LB         TCGA-ZG-A9LM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9LN         TCGA-ZG-A9LS         TCGA-ZG-A9LU 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9LY         TCGA-ZG-A9LZ         TCGA-ZG-A9M4 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9MC         TCGA-ZG-A9N3         TCGA-ZG-A9ND 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D61V8, continuous
D61V9, continuous
D61V10, continuous
D61V11, continuous
D61V12, continuous
D61V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       0                         0     0
  11Q LOSS WILD-TYPE     2                         7   146
D61V14, multiclass

Clustering(62) Variable = 12P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    47   0
  12P LOSS WILD-TYPE 426   8
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                47                434 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                  8 
$`12P LOSS MUTATED`
TCGA-2A-A8VT TCGA-2A-A8W3 TCGA-CH-5744 TCGA-CH-5751 TCGA-CH-5766 TCGA-EJ-5510 
       32.71        25.35         1.97        35.01         1.02        36.69 
TCGA-EJ-5514 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-7781 TCGA-EJ-7784 
       36.23        64.50        68.35        38.76        23.90        25.68 
TCGA-EJ-8472 TCGA-EJ-A7NH TCGA-EJ-A8FS TCGA-G9-6364 TCGA-G9-6379 TCGA-G9-7521 
       24.85        15.58         8.75        39.39        58.45        30.97 
TCGA-HC-8262 TCGA-HC-A48F TCGA-HC-A6AL TCGA-HI-7168 TCGA-J4-A67M TCGA-J9-A52B 
       22.32        22.36         2.20        78.61        30.94        13.87 
TCGA-KC-A4BV TCGA-KC-A7FA TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A7AZ TCGA-KK-A8I4 
       43.66        19.66        54.54       113.33        49.94        67.99 
TCGA-KK-A8IA TCGA-M7-A725 TCGA-MG-AAMC TCGA-V1-A8MF TCGA-V1-A8WV TCGA-VP-A87J 
       63.48        18.84         5.69        41.23        22.55        53.36 
TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-YL-A8SC TCGA-YL-A8SJ TCGA-YL-A9WK TCGA-ZG-A9L5 
       44.88        45.47        41.46        45.86        62.37        29.85 
TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       12.43        16.96        19.04        17.98        11.47 

$`12P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-AAYF 
       20.42        43.79        22.06        33.96         3.68        31.96 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       30.31        20.22        11.51         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
        1.02        12.99        13.97        24.03         1.02        13.02 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       31.00         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
        1.02        23.01        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 
       27.19        23.90        38.93        48.13        48.53        38.53 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5524 
       60.23        46.55        47.80        52.27        51.88        43.07 
TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
       27.68         6.28        24.39        38.37        25.87        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        77.16        76.41        38.10        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        47.44        45.30        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       52.93        38.96        27.91        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV 
       22.55        17.95         1.58        15.88         1.15         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        1.78         2.01         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       12.30        33.01        25.32        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       11.77        13.55        27.12         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       44.35        21.86         8.65         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 
       56.28        44.68        86.40       115.86        30.02       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
       67.59       115.13        49.25        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7B0 
       52.93        58.36        27.02        34.65        51.68        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        20.94       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       34.85        25.08        29.23         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MG 
      122.17        86.14        18.12        11.90        13.32        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       30.38        15.58         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87K TCGA-WW-A8ZI 
       55.56        60.92        66.97        21.80        42.94        14.76 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        53.06        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        60.99 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
       10.13         4.27        11.67        37.94        36.43        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC 
       20.28        19.17         3.78        12.16        22.75        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1.02               0.72 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            113.33             165.17 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             30.97              26.17 
[1] "1.0 - 113.3 (31.0)" "0.7 - 165.2 (26.2)"
[1] "hr="   "8e+07"
D62V2, continuous
                    vv
clus                  T2  T3  T4
  12P LOSS MUTATED    10  34   3
  12P LOSS WILD-TYPE 178 247   7
D62V3, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T2               10                178
  T3               34                247
  T4                3                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    30  17
  12P LOSS WILD-TYPE 308  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     30   17
  12P LOSS WILD-TYPE  308   58
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               30                308
  1               17                 58
[1] 2 2
[1] FALSE
D62V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  47
  12P LOSS WILD-TYPE  14 421
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   47
  12P LOSS WILD-TYPE   14  421
                                        clus
vv                                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  47                421
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    28  15   1   3
  12P LOSS WILD-TYPE 282 123   4  12
D62V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               28                282
  R1               15                123
  R2                1                  4
  RX                3                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, continuous
D62V8, continuous
D62V9, continuous
D62V10, continuous
D62V11, continuous
D62V12, continuous
D62V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0    12
  12P LOSS WILD-TYPE     2                         7   134
D62V14, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   12                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = 12Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    19   0
  12Q LOSS WILD-TYPE 454   8
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                19                462 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 0                  8 
$`12Q LOSS MUTATED`
TCGA-CH-5751 TCGA-EJ-5510 TCGA-EJ-5514 TCGA-EJ-5526 TCGA-EJ-7781 TCGA-EJ-7784 
       35.01        36.69        36.23        38.76        23.90        25.68 
TCGA-G9-7521 TCGA-HC-8216 TCGA-HI-7168 TCGA-J9-A52B TCGA-KC-A4BV TCGA-KC-A7FA 
       30.97        22.42        78.61        13.87        43.66        19.66 
TCGA-KK-A6E1 TCGA-KK-A7AZ TCGA-KK-A8IA TCGA-MG-AAMC TCGA-V1-A8WV TCGA-VP-AA1N 
       54.54        49.94        63.48         5.69        22.55        44.88 
TCGA-ZG-A9M4 
       17.98 

$`12Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       38.93        48.13        48.53        38.53        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
       27.68         6.28        24.39        38.37        25.87        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       38.96        27.91        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        9.53        25.48        18.84        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C 
       14.37        20.28        11.77        13.55        27.12         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD 
       59.67        19.96        44.35        21.86         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       30.02       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       34.65        51.68        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       30.38        15.58         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       37.25        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
        4.27        11.67        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        22.75        14.96        11.47        13.48         4.34 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              5.69               0.72 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             78.61             165.17 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            35.010             26.365 
[1] "5.7 - 78.6 (35.0)"  "0.7 - 165.2 (26.4)"
[1] "hr="     "2.6e+07"
D63V2, continuous
                    vv
clus                  T2  T3  T4
  12Q LOSS MUTATED     4  14   1
  12Q LOSS WILD-TYPE 184 267   9
D63V3, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T2                4                184
  T3               14                267
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    12   7
  12Q LOSS WILD-TYPE 326  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     12    7
  12Q LOSS WILD-TYPE  326   68
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               12                326
  1                7                 68
[1] 2 2
[1] FALSE
D63V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  19
  12Q LOSS WILD-TYPE  14 449
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   19
  12Q LOSS WILD-TYPE   14  449
                                        clus
vv                                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  19                449
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    13   4   0   2
  12Q LOSS WILD-TYPE 297 134   5  13
D63V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               13                297
  R1                4                134
  R2                0                  5
  RX                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, continuous
D63V8, continuous
D63V9, continuous
D63V10, continuous
D63V11, continuous
D63V12, continuous
D63V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0     7
  12Q LOSS WILD-TYPE     2                         7   139
D63V14, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    7                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 13Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    75   0
  13Q LOSS WILD-TYPE 398   8
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                75                406 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  8 
$`13Q LOSS MUTATED`
TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5751 TCGA-CH-5771 TCGA-CH-5788 TCGA-EJ-5495 
       11.51         2.99        35.01        13.02        26.99        33.11 
TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5521 
       28.93        23.90        48.53        36.23        46.55        51.88 
TCGA-EJ-5525 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7786 
       36.66        25.35        33.83        23.90        25.87        14.53 
TCGA-EJ-8472 TCGA-EJ-A46D TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-FC-7961 TCGA-G9-6329 
       24.85        20.58         8.22        15.58        15.42        41.62 
TCGA-G9-6378 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-8266 
       37.97        38.96        27.91        30.97        40.08         1.15 
TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AS TCGA-HI-7168 TCGA-J9-A52B 
        0.76         2.01         1.61         1.45        78.61        13.87 
TCGA-J9-A52E TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7B4 
       10.62        54.54       113.33        67.07        58.19        20.94 
TCGA-KK-A8IA TCGA-KK-A8IG TCGA-KK-A8IH TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9O7 
       63.48        82.36        66.18        22.55        58.39        79.73 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OL TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87D 
        6.71        20.91        19.36        75.91       109.58        60.92 
TCGA-XJ-A9DI TCGA-XK-AAIV TCGA-YJ-A8SW TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC 
       48.03        37.25         4.87        60.56        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ 
       45.14        45.86        46.29        32.45       114.38        62.79 
TCGA-YL-A9WK TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       62.37         4.27        37.94        36.43        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9NI 
       12.43        19.04         4.34 

$`13Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5738 TCGA-CH-5739 
       25.35        31.96        30.31        20.22         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       13.02        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
        2.04        15.98         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       29.00        27.16        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       44.88        26.30        45.73        30.31        27.19        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 
       48.13        36.69        38.53        60.23        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       64.50        68.35        43.07        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7321 TCGA-EJ-7325 
       83.57        36.13        37.81        33.14        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 
       30.35        27.68         6.28        24.39        38.37        25.68 
TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        77.16        76.41        38.10        25.18 
TCGA-EJ-A46B TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       21.60        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
        7.56        11.61        28.70        14.20         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.31         4.77        28.41        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       16.24         1.78        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       40.31        26.66        31.50        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7522 
       58.22        56.75        64.18        50.73        52.93        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
       22.36         1.78         2.20        17.42         2.33         3.48 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       18.84        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CM 
       11.77        13.55        27.12         5.85        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A7AP TCGA-KK-A7AQ 
      165.17        67.59       115.13        49.25         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       26.43       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9OF TCGA-V1-A9OH 
       52.08        30.38        15.58         6.64        38.93        41.19 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       25.78        16.31       111.39        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        66.97        21.80        53.36        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       42.08         9.04         2.99        31.99        31.96        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       32.19        25.48        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SP 
       71.77        62.14        16.83        28.77        53.06        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
        8.98        14.04        53.36        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 
       28.34         3.09        14.53        13.28        10.13        11.67 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       29.85        22.59         3.78        16.96        12.16        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       17.98        14.96        11.47        13.48 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.76               0.72 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            114.38             165.17 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             33.11              25.76 
[1] "0.8 - 114.4 (33.1)" "0.7 - 165.2 (25.8)"
[1] "hr="     "9.1e+07"
D64V2, continuous
                    vv
clus                  T2  T3  T4
  13Q LOSS MUTATED    16  56   3
  13Q LOSS WILD-TYPE 172 225   7
D64V3, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T2               16                172
  T3               56                225
  T4                3                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    50  20
  13Q LOSS WILD-TYPE 288  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     50   20
  13Q LOSS WILD-TYPE  288   55
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               50                288
  1               20                 55
[1] 2 2
[1] FALSE
D64V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  74
  13Q LOSS WILD-TYPE  13 394
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   74
  13Q LOSS WILD-TYPE   13  394
                                        clus
vv                                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  74                394
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    38  32   0   3
  13Q LOSS WILD-TYPE 272 106   5  12
D64V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               38                272
  R1               32                106
  R2                0                  5
  RX                3                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, continuous
D64V8, continuous
D64V9, continuous
D64V10, continuous
D64V11, continuous
D64V12, continuous
D64V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         2    19
  13Q LOSS WILD-TYPE     2                         5   127
D64V14, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   19                127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 14Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    24   1
  14Q LOSS WILD-TYPE 449   7
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                456 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                  7 
$`14Q LOSS MUTATED`
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-G9-6361 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-7523 
       25.87        25.68        46.52        50.73        30.97        28.18 
TCGA-HC-7213 TCGA-HC-7821 TCGA-HC-A76W TCGA-HI-7171 TCGA-J4-A67O TCGA-KK-A8IA 
       40.08        31.43         7.00        43.69        27.58        63.48 
TCGA-VP-A875 TCGA-VP-A87K TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SJ TCGA-YL-A8SL 
       75.91        42.94        71.77        56.52        45.86        32.45 
TCGA-YL-A8SQ TCGA-YL-A9WX TCGA-ZG-A9KY TCGA-ZG-A9L5 TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       62.79        49.91         4.27        29.85        22.75        17.98 
TCGA-ZG-A9N3 
       11.47 

$`14Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       24.39        23.90        38.37        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       47.15        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 
       64.18        52.93        38.96        27.91        35.34        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
        0.79        28.60         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 
       30.51        30.84        17.85        24.56        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        3.48         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
       25.48        18.84        78.61        88.24        82.92        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67Q 
       12.30        33.01        25.32        30.94        16.54        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       11.77        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC 
       21.96        65.82        31.79        32.91         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF 
       48.72        62.14        60.56        16.83        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR 
       28.77        53.06        46.29       114.38        71.34         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WY 
       14.04        53.36        60.99        62.37        24.33        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       16.96        19.04        12.16        14.96        13.48         4.34 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              4.27               0.72 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             75.91             165.17 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             32.45              25.76 
[1] "4.3 - 75.9 (32.5)"  "0.7 - 165.2 (25.8)"
[1] "hr=" "2.5"
D65V2, continuous
                    vv
clus                  T2  T3  T4
  14Q LOSS MUTATED     2  21   2
  14Q LOSS WILD-TYPE 186 260   8
D65V3, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T2                2                186
  T3               21                260
  T4                2                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V4, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    16   9
  14Q LOSS WILD-TYPE 322  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     16    9
  14Q LOSS WILD-TYPE  322   66
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               16                322
  1                9                 66
[1] 2 2
[1] FALSE
D65V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  24
  14Q LOSS WILD-TYPE  13 444
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   24
  14Q LOSS WILD-TYPE   13  444
                                        clus
vv                                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  24                444
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED     9  14   0   1
  14Q LOSS WILD-TYPE 301 124   5  14
D65V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0                9                301
  R1               14                124
  R2                0                  5
  RX                1                 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"
D65V7, continuous
D65V8, continuous
D65V9, continuous
D65V10, continuous
D65V11, continuous
D65V12, continuous
D65V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       0                         0     7
  14Q LOSS WILD-TYPE     2                         7   139
D65V14, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    7                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 15Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    35   1
  15Q LOSS WILD-TYPE 438   7
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                36                445 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                  7 
$`15Q LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5753 TCGA-EJ-5507 TCGA-EJ-7783 TCGA-FC-A4JI TCGA-G9-7521 
       35.01         1.02        23.90        25.87        13.45        30.97 
TCGA-HC-7213 TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7821 TCGA-HC-8216 TCGA-HI-7168 
       40.08         1.97        25.71        31.43        22.42        78.61 
TCGA-HI-7171 TCGA-J9-A52E TCGA-J9-A8CL TCGA-KC-A7FA TCGA-KK-A59Z TCGA-KK-A6E0 
       43.69        10.62        13.32        19.66        86.40        30.02 
TCGA-KK-A8IA TCGA-V1-A8WS TCGA-V1-A9O7 TCGA-V1-A9OL TCGA-VP-A872 TCGA-XK-AAJA 
       63.48        15.58        79.73        19.36       111.39        30.58 
TCGA-XK-AAJT TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SQ TCGA-ZG-A9KY TCGA-ZG-A9L0 
       47.15        71.77        56.52        62.79         4.27        11.67 
TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       29.85        20.28        12.43        22.75        17.98        11.47 

$`15Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 
       24.03         1.02        13.02        31.00         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 
       45.73        28.93        30.31        27.19        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V 
        4.31         4.77        28.41        15.42        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       52.93        38.96        27.91        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
        0.79        28.60         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 
       23.70        24.59        26.04        17.16        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       17.85        24.56        19.36        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       88.24        82.92        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
       27.12        13.87         5.85        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
      115.86        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ 
       58.39         6.71        20.91        38.93        41.19        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87         4.70         5.82         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       16.31        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        41.49        41.39        36.95 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC 
       51.45        48.72        62.14        60.56        16.83        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        71.34         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LB 
       13.28        10.13        37.94        36.43        22.59        19.17 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND 
        3.78        16.96        19.04        12.16        14.96        13.48 
TCGA-ZG-A9NI 
        4.34 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.02               0.72 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            111.39             165.17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             25.79              26.99 
[1] "1.0 - 111.4 (25.8)" "0.7 - 165.2 (27.0)"
[1] "hr=" "2.2"
D66V2, continuous
                    vv
clus                  T2  T3  T4
  15Q LOSS MUTATED     2  31   3
  15Q LOSS WILD-TYPE 186 250   7
D66V3, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T2                2                186
  T3               31                250
  T4                3                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V4, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20  13
  15Q LOSS WILD-TYPE 318  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20   13
  15Q LOSS WILD-TYPE  318   62
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               20                318
  1               13                 62
[1] 2 2
[1] FALSE
D66V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  35
  15Q LOSS WILD-TYPE  13 433
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   35
  15Q LOSS WILD-TYPE   13  433
                                        clus
vv                                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  35                433
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    18  16   0   1
  15Q LOSS WILD-TYPE 292 122   5  14
D66V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               18                292
  R1               16                122
  R2                0                  5
  RX                1                 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"
D66V7, continuous
D66V8, continuous
D66V9, continuous
D66V10, continuous
D66V11, continuous
D66V12, continuous
D66V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         0    10
  15Q LOSS WILD-TYPE     2                         7   136
D66V14, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   10                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = 16P LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    30   0
  16P LOSS WILD-TYPE 443   8
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                30                451 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                  8 
$`16P LOSS MUTATED`
TCGA-CH-5739 TCGA-EJ-5498 TCGA-EJ-5514 TCGA-EJ-7123 TCGA-EJ-7781 TCGA-EJ-7784 
       22.06        29.79        36.23        74.10        23.90        25.68 
TCGA-EJ-8469 TCGA-EJ-A7NH TCGA-G9-6329 TCGA-G9-7523 TCGA-HC-7078 TCGA-HC-7749 
       76.41        15.58        41.62        28.18        65.26         1.97 
TCGA-HC-A4ZV TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-J4-A83I TCGA-J9-A8CL 
        0.76         1.25         4.41         7.00        22.52        13.32 
TCGA-KC-A7FA TCGA-KK-A59Z TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A8IG TCGA-V1-A9O7 
       19.66        86.40        67.07         6.44        82.36        79.73 
TCGA-V1-A9OA TCGA-VP-AA1N TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A8SQ TCGA-ZG-A9LZ 
       20.91        44.88        71.77        45.86        62.79        22.75 

$`16P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
        6.97         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       33.11        19.56        13.32        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        36.69        48.53        38.53        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       29.06        88.34        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
       27.68         6.28        24.39        38.37        25.87        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       23.05        19.92        77.16        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 
       13.45        22.36        17.23        16.24         1.78        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       35.34        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
        3.68        19.76         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 
        1.48         1.68        23.70        24.59        26.04        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        2.33         3.48         1.45         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       16.83        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       11.77        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       44.35        43.66        21.86         8.65         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        56.28        44.68       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E8 
      165.17        67.59       115.13        49.25       113.33        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II 
        2.73        67.43        69.27        26.43        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OF 
       15.58        22.55         6.64        58.39         6.71        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       48.72        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        53.06        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34         8.98        14.04        53.36        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
       10.13         4.27        11.67        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.76               0.72 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             86.40             165.17 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             26.93              26.66 
[1] "0.8 - 86.4 (26.9)"  "0.7 - 165.2 (26.7)"
[1] "hr="     "7.8e+07"
D67V2, continuous
                    vv
clus                  T2  T3  T4
  16P LOSS MUTATED    10  20   0
  16P LOSS WILD-TYPE 178 261  10
D67V3, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T2               10                178
  T3               20                261
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V4, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    24   3
  16P LOSS WILD-TYPE 314  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     24    3
  16P LOSS WILD-TYPE  314   72
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               24                314
  1                3                 72
[1] 2 2
[1] FALSE
D67V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0  30
  16P LOSS WILD-TYPE  14 438
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   30
  16P LOSS WILD-TYPE   14  438
                                        clus
vv                                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  30                438
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    17  12   0   1
  16P LOSS WILD-TYPE 293 126   5  14
D67V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               17                293
  R1               12                126
  R2                0                  5
  RX                1                 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"
D67V7, continuous
D67V8, continuous
D67V9, continuous
D67V10, continuous
D67V11, continuous
D67V12, continuous
D67V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         0     9
  16P LOSS WILD-TYPE     2                         7   137
D67V14, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    9                137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 16Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   101   1
  16Q LOSS WILD-TYPE 372   7
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               102                379 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                  7 
$`16Q LOSS MUTATED`
TCGA-2A-A8VT TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5764 TCGA-CH-5788 TCGA-CH-5791 
       32.71        22.06        35.01         1.02        26.99        33.01 
TCGA-EJ-5495 TCGA-EJ-5498 TCGA-EJ-5514 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-7123 
       33.11        29.79        36.23        36.66        39.75        74.10 
TCGA-EJ-7312 TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 
       36.13        33.83        30.35        23.90        25.87        25.68 
TCGA-EJ-7789 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-A46F TCGA-EJ-A7NH TCGA-EJ-A7NM 
       18.15        76.41        38.10        25.74        15.58         4.21 
TCGA-FC-7961 TCGA-FC-A5OB TCGA-G9-6329 TCGA-G9-6343 TCGA-G9-6362 TCGA-G9-6384 
       15.42        22.36        41.62        18.21        47.44        25.15 
TCGA-G9-6496 TCGA-G9-7521 TCGA-G9-7523 TCGA-HC-7078 TCGA-HC-7213 TCGA-HC-7736 
       56.75        30.97        28.18        65.26        40.08         0.72 
TCGA-HC-7742 TCGA-HC-7749 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A4ZV 
        1.48         1.97        31.43        22.42        22.36         0.76 
TCGA-HC-A632 TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A8D0 TCGA-HI-7168 
        2.01         1.25         4.41         7.00        25.48        78.61 
TCGA-HI-7171 TCGA-J4-A83I TCGA-J9-A52B TCGA-J9-A8CL TCGA-J9-A8CP TCGA-KC-A4BV 
       43.69        22.52        13.87        13.32        12.69        43.66 
TCGA-KC-A7FA TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP 
       19.66        86.40       115.86       113.33        67.07         6.44 
TCGA-KK-A7AU TCGA-KK-A7B4 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IF 
       58.36        20.94        21.96        65.82        31.79        26.43 
TCGA-KK-A8IG TCGA-KK-A8IK TCGA-QU-A6IO TCGA-V1-A8MG TCGA-V1-A8WV TCGA-V1-A8X3 
       82.36        51.39       122.17        28.18        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9ZI TCGA-VN-A88M TCGA-VN-A88N 
       58.39        79.73        20.91         4.70         6.21        15.52 
TCGA-VN-A88Q TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83H TCGA-XK-AAIR 
       44.91        42.94        44.88        45.47        42.08        31.96 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-YL-A8HO TCGA-YL-A8SC TCGA-YL-A8SJ TCGA-YL-A8SL 
       41.39        36.95        71.77        41.46        45.86        32.45 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WK TCGA-YL-A9WX TCGA-ZG-A9L4 TCGA-ZG-A9L9 
       62.79         8.98        62.37        49.91        36.43        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.17        12.43        22.75        17.98        14.96        11.47 

$`16Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         2.99         6.97 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       13.02        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       12.00        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 
       13.02        15.98         9.99        32.02         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       27.16        19.56        13.32        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        36.69        48.53        38.53        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       38.76        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7321 
       93.70        83.57        37.81        33.14        25.35        27.09 
TCGA-EJ-7325 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7785 
       35.18        27.68         6.28        24.39        38.37        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.53        14.14        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       19.92        77.16        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A8FN 
       28.70         8.22        14.20         6.48        15.65        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 
       28.41        13.45        17.23        16.24         1.78        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6347 
       81.04        67.99        66.67        83.87        55.76        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       27.91        35.34        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       30.94         3.68        19.76         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
       38.17        44.55         2.10        31.69        23.57         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        26.04        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       30.84        17.85        24.56        19.36        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       15.88         1.15         1.78         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D1 
        2.33         3.48         1.45         4.93         9.53        18.84 
TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       88.24        82.92        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K 
        6.02        25.28        27.91        16.83        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-KC-A4BL TCGA-KC-A4BN 
        5.85        10.62        15.22        40.67        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       19.96        44.35        21.86         8.65         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
      113.10        56.28        44.68        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AV 
       67.59       115.13        49.25        58.19        52.93        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       29.56        67.99       101.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL 
       67.43        69.27        66.18       113.98        51.25        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      140.19        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       30.38        15.58         6.71        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       17.75        49.87         5.82         8.84        25.51        24.53 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        25.78        16.31       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR 
       66.97        21.80        53.36        14.76        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       37.05        38.04        48.03         9.04         2.99        31.99 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJT TCGA-XK-AAJU 
       37.25        40.04        41.49        30.58        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       48.72        62.14        60.56        16.83        56.52        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A9WH 
       28.77        53.06        46.29       114.38        71.34        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       53.36        60.99        24.33        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L5 
       13.28        10.13         4.27        11.67        37.94        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9ND 
       22.59         3.78        16.96        19.04        12.16        13.48 
TCGA-ZG-A9NI 
        4.34 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.72               0.79 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            122.17             165.17 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             30.07              25.78 
[1] "0.7 - 122.2 (30.1)" "0.8 - 165.2 (25.8)"
[1] "hr=" "2.5"
D68V2, continuous
                    vv
clus                  T2  T3  T4
  16Q LOSS MUTATED    26  73   3
  16Q LOSS WILD-TYPE 162 208   7
D68V3, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T2               26                162
  T3               73                208
  T4                3                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V4, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    71  23
  16Q LOSS WILD-TYPE 267  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     71   23
  16Q LOSS WILD-TYPE  267   52
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               71                267
  1               23                 52
[1] 2 2
[1] FALSE
D68V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3  99
  16Q LOSS WILD-TYPE  11 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   99
  16Q LOSS WILD-TYPE   11  369
                                        clus
vv                                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                3                 11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  99                369
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    56  40   0   2
  16Q LOSS WILD-TYPE 254  98   5  13
D68V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               56                254
  R1               40                 98
  R2                0                  5
  RX                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, continuous
D68V8, continuous
D68V9, continuous
D68V10, continuous
D68V11, continuous
D68V12, continuous
D68V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         1    29
  16Q LOSS WILD-TYPE     2                         6   117
D68V14, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   29                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = 17P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    72   1
  17P LOSS WILD-TYPE 401   7
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                73                408 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                  7 
$`17P LOSS MUTATED`
TCGA-4L-AA1F TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5764 TCGA-CH-5790 TCGA-EJ-5507 
       11.51         2.04         0.92         1.02        32.02        23.90 
TCGA-EJ-5514 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5526 TCGA-EJ-7315 TCGA-EJ-7781 
       36.23        64.50        51.88        38.76        33.14        23.90 
TCGA-EJ-7797 TCGA-EJ-A46F TCGA-EJ-A7NH TCGA-FC-A4JI TCGA-G9-6373 TCGA-G9-6377 
       19.92        25.74        15.58        13.45        26.66        31.50 
TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S7 
       58.22        50.73        52.93        38.96        30.97        23.93 
TCGA-HC-7078 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-8266 
       65.26        40.08         1.68         1.48         1.68         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HI-7168 TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A59Z 
       22.36         0.76        78.61        13.87        10.62        86.40 
TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7B4 
      115.86        54.54       115.13       113.33         6.44        20.94 
TCGA-KK-A8I6 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8IG TCGA-KK-A8IK TCGA-M7-A725 
       21.96        63.48        67.43        82.36        51.39        18.84 
TCGA-V1-A8ML TCGA-V1-A8WS TCGA-V1-A9Z7 TCGA-VP-A875 TCGA-VP-A87C TCGA-VP-A87D 
       14.73        15.58         4.27        75.91        55.56        60.92 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-XK-AAJA TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       42.94        44.88        30.58        49.02        51.45        71.77 
TCGA-YL-A8SB TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-ZG-A9L0 
       56.52        46.29        32.45        62.79        14.04        11.67 
TCGA-ZG-A9L4 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9M4 
       36.43        20.28        19.17        12.43        19.04        17.98 
TCGA-ZG-A9N3 
       11.47 

$`17P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5762 
        1.02        13.02        35.01        31.00         1.02        44.02 
TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       12.00        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5791 TCGA-CH-5792 
       13.02        15.98        26.99         9.99        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       27.19        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5522 TCGA-EJ-5524 
       60.23        46.55        47.80        52.27        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        6.28        24.39        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       23.05        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       21.60        20.58        17.23        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ 
        7.56        11.61        28.70         8.22        14.20         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB 
        4.54         4.31         4.77        28.41        15.42        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       39.95        38.01        40.31        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       27.29        56.75        64.18        27.91        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        26.01         6.08        30.94         3.68        19.76 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
       28.60         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
       31.69        23.57        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        9.53        25.48        18.84        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C 
       14.37        20.28        11.77        13.55        27.12         5.85 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6E0 
        8.88        11.57       113.10        56.28        44.68        30.02 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      165.17        67.59        49.25        67.07        58.19        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I7 
       34.95        36.13        29.56        67.99       101.79        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH 
       31.79        32.91         2.73        69.27        26.43        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
      113.98        51.25        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC 
       12.62        13.15        34.85        25.08        29.23         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 
       19.36        12.20        15.65         8.42         5.59         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78        16.31       111.39       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-WW-A8ZI TCGA-X4-A8KQ 
       85.18        66.97        21.80        53.36        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       41.49        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 
       25.48         4.87        52.96        48.72        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       16.83        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
      114.38        71.34         8.98        53.36        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LN 
       10.13         4.27        37.94        29.85        22.59         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       16.96        12.16        22.75        14.96        13.48         4.34 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.76               0.72 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            115.86             165.17 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             30.97              26.17 
[1] "0.8 - 115.9 (31.0)" "0.7 - 165.2 (26.2)"
[1] "hr=" "2"  
D69V2, continuous
                    vv
clus                  T2  T3  T4
  17P LOSS MUTATED    15  57   1
  17P LOSS WILD-TYPE 173 224   9
D69V3, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T2               15                173
  T3               57                224
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V4, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    48  21
  17P LOSS WILD-TYPE 290  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     48   21
  17P LOSS WILD-TYPE  290   54
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               48                290
  1               21                 54
[1] 2 2
[1] FALSE
D69V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1  72
  17P LOSS WILD-TYPE  13 396
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   72
  17P LOSS WILD-TYPE   13  396
                                        clus
vv                                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  72                396
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED    40  31   0   2
  17P LOSS WILD-TYPE 270 107   5  13
D69V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               40                270
  R1               31                107
  R2                0                  5
  RX                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, continuous
D69V8, continuous
D69V9, continuous
D69V10, continuous
D69V11, continuous
D69V12, continuous
D69V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         0    22
  17P LOSS WILD-TYPE     2                         7   124
D69V14, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   22                124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = 17Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    18   1
  17Q LOSS WILD-TYPE 455   7
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                462 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                  7 
$`17Q LOSS MUTATED`
TCGA-G9-6499 TCGA-HC-7213 TCGA-HC-7744 TCGA-HC-A48F TCGA-J9-A52E TCGA-KK-A6E4 
       50.73        40.08         1.68        22.36        10.62       115.13 
TCGA-KK-A7AP TCGA-KK-A8IA TCGA-KK-A8IG TCGA-M7-A725 TCGA-V1-A9OL TCGA-VP-A875 
        6.44        63.48        82.36        18.84        19.36        75.91 
TCGA-VP-AA1N TCGA-XK-AAJA TCGA-YL-A8HO TCGA-YL-A8SQ TCGA-ZG-A9L4 TCGA-ZG-A9LM 
       44.88        30.58        71.77        62.79        36.43        12.43 
TCGA-ZG-A9M4 
       17.98 

$`17Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       28.60         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 
        2.10        31.69        23.57         1.48        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
        1.58        15.88         1.15         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 
      115.86        30.02        54.54       165.17        67.59        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        67.07        58.19        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       31.79        32.91         2.73        67.43        69.27        26.43 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       30.38        15.58        22.55         6.64        58.39        79.73 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT 
        6.71        20.91        38.93        41.19        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      111.39       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       60.92        66.97        21.80        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        41.49        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       48.72        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        71.34         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L5 
       13.28        10.13         4.27        11.67        37.94        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       22.59        20.28        19.17         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        22.75        14.96        11.47        13.48         4.34 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              1.68               0.72 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            115.13             165.17 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            36.430             26.365 
[1] "1.7 - 115.1 (36.4)" "0.7 - 165.2 (26.4)"
[1] "hr=" "1.5"
D70V2, continuous
                    vv
clus                  T2  T3  T4
  17Q LOSS MUTATED     2  17   0
  17Q LOSS WILD-TYPE 186 264  10
D70V3, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T2                2                186
  T3               17                264
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V4, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    14   5
  17Q LOSS WILD-TYPE 324  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     14    5
  17Q LOSS WILD-TYPE  324   70
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               14                324
  1                5                 70
[1] 2 2
[1] FALSE
D70V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  19
  17Q LOSS WILD-TYPE  14 449
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   19
  17Q LOSS WILD-TYPE   14  449
                                        clus
vv                                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  19                449
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED     7  11   0   1
  17Q LOSS WILD-TYPE 303 127   5  14
D70V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                7                303
  R1               11                127
  R2                0                  5
  RX                1                 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"
D70V7, continuous
D70V8, continuous
D70V9, continuous
D70V10, continuous
D70V11, continuous
D70V12, continuous
D70V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0     3
  17Q LOSS WILD-TYPE     2                         7   143
D70V14, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    3                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = 18P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    64   3
  18P LOSS WILD-TYPE 409   5
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                414 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 3                  5 
$`18P LOSS MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5772 TCGA-CH-5788 
       32.71        11.51        35.01         0.92        15.98        26.99 
TCGA-CH-5791 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-7781 TCGA-EJ-8472 
       33.01        36.23        52.27        64.50        23.90        24.85 
TCGA-EJ-A65B TCGA-EJ-A7NF TCGA-G9-6354 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-7523 
       23.34         8.22        49.35        26.66        31.50        28.18 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 
       26.01        23.93        65.26         0.79        40.08         1.68 
TCGA-HC-7736 TCGA-HC-7745 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-A48F TCGA-HC-A631 
        0.72        23.70        24.56        31.43        22.36         1.78 
TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A8CY TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 
        2.01         7.00         9.53        78.61        82.92        43.69 
TCGA-J9-A8CL TCGA-KC-A7FA TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E7 TCGA-KK-A7B4 
       13.32        19.66        86.40       115.86        67.07        20.94 
TCGA-KK-A8I7 TCGA-KK-A8IB TCGA-KK-A8II TCGA-M7-A724 TCGA-TP-A8TV TCGA-V1-A8MJ 
       65.82         2.73       113.98        29.23        13.32        40.44 
TCGA-V1-A8WV TCGA-V1-A9ZI TCGA-VN-A88P TCGA-VP-A872 TCGA-WW-A8ZI TCGA-XJ-A83G 
       22.55         4.70        41.42       111.39        14.76        38.04 
TCGA-XK-AAIV TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A8SO 
       37.25        49.02        48.72        71.77        45.86       114.38 
TCGA-YL-A9WK TCGA-ZG-A9L2 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       62.37        37.94        29.85        20.28        19.17        12.43 
TCGA-ZG-A9LU 
       19.04 

$`18P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 
       13.02        31.00         1.02         2.04        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02         9.99        32.02         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 
       38.93        48.13        36.69        48.53        38.53        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       46.55        47.80        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
       27.68         6.28        24.39        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       23.80        21.96        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NG TCGA-EJ-A7NH 
       14.83         7.56        11.61        28.70        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 
       18.21        68.68        49.81        46.16        50.70        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6379 
       40.18        39.95        38.01        40.31        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 
       52.93        38.96        27.91        30.97        35.34        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 
        6.08        30.94         3.68        19.76         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7231 TCGA-HC-7232 
       37.35        14.47        28.54        28.60         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       44.55         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       30.84        17.85        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       15.88         1.15         0.76         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
        2.33         3.48         1.45         1.25         4.41         4.93 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       25.48        18.84        88.24        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM 
       13.55        27.12        13.87         5.85        10.62        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       43.66        21.86         8.65         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       56.28        44.68        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
      115.13        49.25       113.33        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        67.99       101.79        21.96 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       31.79        32.91        63.48        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       82.36        66.18        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MK 
       86.14        18.12        11.90        41.23        28.18        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        58.39        79.73         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I 
        4.27         6.15        17.75        49.87         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q 
       25.51        24.53         6.21        15.52        15.81        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78        16.31        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        44.88        45.47        32.19         3.91        37.05 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HL 
       51.81        32.19        25.48         4.87        52.96        51.45 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SQ 
       28.77        53.06        46.29        32.45        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
        8.98        14.04        53.36        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       28.34         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY 
       11.67        36.43        22.59         3.78        16.96        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.72               0.76 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            115.86             165.17 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             28.18              26.17 
[1] "0.7 - 115.9 (28.2)" "0.8 - 165.2 (26.2)"
[1] "hr=" "2.5"
D71V2, continuous
                    vv
clus                  T2  T3  T4
  18P LOSS MUTATED    17  46   4
  18P LOSS WILD-TYPE 171 235   6
D71V3, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T2               17                171
  T3               46                235
  T4                4                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V4, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    46  16
  18P LOSS WILD-TYPE 292  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     46   16
  18P LOSS WILD-TYPE  292   59
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               46                292
  1               16                 59
[1] 2 2
[1] FALSE
D71V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  64
  18P LOSS WILD-TYPE  11 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   64
  18P LOSS WILD-TYPE   11  404
                                        clus
vv                                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                3                 11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  64                404
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    33  31   0   0
  18P LOSS WILD-TYPE 277 107   5  15
D71V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               33                277
  R1               31                107
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, continuous
D71V8, continuous
D71V9, continuous
D71V10, continuous
D71V11, continuous
D71V12, continuous
D71V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         0    22
  18P LOSS WILD-TYPE     2                         7   124
D71V14, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   22                124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = 18Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    94   3
  18Q LOSS WILD-TYPE 379   5
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                97                384 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                  5 
$`18Q LOSS MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5772 
       32.71        11.51        35.01         2.04         0.92        15.98 
TCGA-CH-5791 TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5524 
       33.01        28.93        23.90        36.23        52.27        43.07 
TCGA-EJ-5525 TCGA-EJ-7781 TCGA-EJ-7794 TCGA-EJ-8472 TCGA-EJ-A65B TCGA-EJ-A7NF 
       36.66        23.90        23.05        24.85        23.34         8.22 
TCGA-EJ-A7NH TCGA-G9-6329 TCGA-G9-6348 TCGA-G9-6354 TCGA-G9-6373 TCGA-G9-6377 
       15.58        41.62        49.81        49.35        26.66        31.50 
TCGA-G9-6378 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7078 TCGA-HC-7211 
       37.97        30.97        28.18        26.01        65.26         0.79 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7820 TCGA-HC-7821 
       40.08         1.68         1.48        23.70        24.56        31.43 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A8CY 
       22.36         0.76         1.78         4.41         7.00         9.53 
TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-A67N TCGA-J9-A8CL TCGA-KC-A7FA 
       78.61        82.92        43.69        16.54        13.32        19.66 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A6E7 
       56.28        86.40       115.86        54.54       113.33        67.07 
TCGA-KK-A7AW TCGA-KK-A7B4 TCGA-KK-A8I7 TCGA-KK-A8IB TCGA-KK-A8IH TCGA-KK-A8II 
       34.65        20.94        65.82         2.73        66.18       113.98 
TCGA-M7-A724 TCGA-M7-A725 TCGA-TP-A8TV TCGA-V1-A8MJ TCGA-V1-A8MU TCGA-V1-A8WV 
       29.23        18.84        13.32        40.44        53.16        22.55 
TCGA-V1-A9O7 TCGA-V1-A9ZI TCGA-VN-A88K TCGA-VN-A88P TCGA-VP-A872 TCGA-VP-A87C 
       79.73         4.70        25.51        41.42       111.39        55.56 
TCGA-WW-A8ZI TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YL-A8HK 
       14.76        37.05        38.04        37.25        47.15        49.02 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8SA TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SQ 
       48.72        71.77        16.83        45.86       114.38        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A9L5 
        8.98        14.04        62.37        49.91        28.34        29.85 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LZ 
       20.28        19.17        12.43        16.96        19.04        22.75 
TCGA-ZG-A9N3 
       11.47 

$`18Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
       13.02        31.00         1.02        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       26.99         9.99        32.02         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 
       26.30        45.73        30.31        27.19        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        48.53        38.53        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       64.50        51.88        68.35        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7797 TCGA-EJ-8468 
       18.15        19.59        17.29         3.75        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       76.41        38.10        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        21.96        23.80        21.96        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       14.20         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       18.21        68.68        46.16        50.70        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       39.95        38.01        40.31        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       27.91        35.34        32.68        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
        3.68        19.76         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       28.54        28.60         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 
        2.10        31.69        23.57         1.68        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        1.45         1.25         4.93        25.48        18.84        88.24 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O 
       20.19        12.30        33.01        25.32        30.94        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.62        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD 
       19.96        44.35        43.66        21.86         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       11.57       113.10        44.68        30.02       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      115.13        49.25        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       27.02        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 
       29.56        67.99       101.79        21.96        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ 
       63.48        67.43        69.27        26.43        82.36        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       13.15        34.85        25.08         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF 
      140.19       122.17        86.14        18.12        11.90        41.23 
TCGA-V1-A8MG TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WN 
       28.18        16.70        14.73        39.29        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       15.58         6.64        58.39         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I 
        4.27         6.15        17.75        49.87         5.82         8.84 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R 
       24.53         6.21        15.52        15.81        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       16.31        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        53.36        42.94        44.88 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       45.47        32.19         3.91        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        31.99        31.96        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       41.39        36.95        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC 
       52.96        51.45        62.14        60.56        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP 
       45.14        28.77        53.06        46.29        32.45        71.34 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        24.33         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
       10.13         4.27        11.67        37.94        36.43        22.59 
TCGA-ZG-A9LN TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
        3.78        12.16        17.98        14.96        13.48         4.34 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.76               0.72 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            115.86             165.17 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            29.230             25.825 
[1] "0.8 - 115.9 (29.2)" "0.7 - 165.2 (25.8)"
[1] "hr=" "1.8"
D72V2, continuous
                    vv
clus                  T2  T3  T4
  18Q LOSS MUTATED    24  70   4
  18Q LOSS WILD-TYPE 164 211   6
D72V3, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T2               24                164
  T3               70                211
  T4                4                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V4, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    61  28
  18Q LOSS WILD-TYPE 277  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     61   28
  18Q LOSS WILD-TYPE  277   47
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               61                277
  1               28                 47
[1] 2 2
[1] FALSE
D72V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3  95
  18Q LOSS WILD-TYPE  11 373
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   95
  18Q LOSS WILD-TYPE   11  373
                                        clus
vv                                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                3                 11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  95                373
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    46  48   0   2
  18Q LOSS WILD-TYPE 264  90   5  13
D72V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               46                264
  R1               48                 90
  R2                0                  5
  RX                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, continuous
D72V8, continuous
D72V9, continuous
D72V10, continuous
D72V11, continuous
D72V12, continuous
D72V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         2    28
  18Q LOSS WILD-TYPE     2                         5   118
D72V14, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   28                118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = 19P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    17   0
  19P LOSS WILD-TYPE 456   8
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                464 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 0                  8 
$`19P LOSS MUTATED`
TCGA-EJ-7328 TCGA-EJ-7781 TCGA-HC-7080 TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CL 
       27.68        23.90        36.36        13.87        10.62        13.32 
TCGA-KC-A7FA TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-TP-A8TV TCGA-XK-AAJA 
       19.66        49.25       113.33        67.07        13.32        30.58 
TCGA-YL-A8HM TCGA-YL-A8SL TCGA-YL-A9WK TCGA-ZG-A9M4 TCGA-ZG-A9NI 
       48.72        32.45        62.37        17.98         4.34 

$`19P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 
       33.83        27.09        35.18        30.35         6.28        24.39 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C 
       14.37        20.28        11.77        13.55        27.12         5.85 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       44.35        43.66        21.86         8.65         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 TCGA-KK-A7AP 
       54.54       165.17        67.59       115.13        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       86.14        18.12        11.90        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        41.49        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        51.45        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       46.29       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        60.99        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC 
        3.78        16.96        19.04        12.16        22.75        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       11.47        13.48 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              4.34               0.72 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            113.33             165.17 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            27.680             26.545 
[1] "4.3 - 113.3 (27.7)" "0.7 - 165.2 (26.5)"
[1] "hr="     "2.6e+07"
D73V2, continuous
                    vv
clus                  T2  T3  T4
  19P LOSS MUTATED     3  14   0
  19P LOSS WILD-TYPE 185 267  10
D73V3, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T2                3                185
  T3               14                267
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V4, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    13   3
  19P LOSS WILD-TYPE 325  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     13    3
  19P LOSS WILD-TYPE  325   72
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               13                325
  1                3                 72
[1] 2 2
[1] FALSE
D73V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0  17
  19P LOSS WILD-TYPE  14 451
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   17
  19P LOSS WILD-TYPE   14  451
                                        clus
vv                                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  17                451
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED     9   8   0   0
  19P LOSS WILD-TYPE 301 130   5  15
D73V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                9                301
  R1                8                130
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, continuous
D73V8, continuous
D73V9, continuous
D73V10, continuous
D73V11, continuous
D73V12, continuous
D73V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         0     3
  19P LOSS WILD-TYPE     2                         7   143
D73V14, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    3                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = 19Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    17   0
  19Q LOSS WILD-TYPE 456   8
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                464 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                  8 
$`19Q LOSS MUTATED`
TCGA-EJ-7328 TCGA-EJ-7781 TCGA-HC-7080 TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CL 
       27.68        23.90        36.36        13.87        10.62        13.32 
TCGA-KC-A7FA TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-TP-A8TV TCGA-XK-AAJA 
       19.66        49.25       113.33        67.07        13.32        30.58 
TCGA-YL-A8HM TCGA-YL-A8SL TCGA-YL-A9WK TCGA-ZG-A9M4 TCGA-ZG-A9NI 
       48.72        32.45        62.37        17.98         4.34 

$`19Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 
       33.83        27.09        35.18        30.35         6.28        24.39 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C 
       14.37        20.28        11.77        13.55        27.12         5.85 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       44.35        43.66        21.86         8.65         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 TCGA-KK-A7AP 
       54.54       165.17        67.59       115.13        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       86.14        18.12        11.90        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        41.49        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        51.45        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       46.29       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        60.99        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC 
        3.78        16.96        19.04        12.16        22.75        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       11.47        13.48 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              4.34               0.72 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            113.33             165.17 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            27.680             26.545 
[1] "4.3 - 113.3 (27.7)" "0.7 - 165.2 (26.5)"
[1] "hr="     "2.6e+07"
D74V2, continuous
                    vv
clus                  T2  T3  T4
  19Q LOSS MUTATED     3  14   0
  19Q LOSS WILD-TYPE 185 267  10
D74V3, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T2                3                185
  T3               14                267
  T4                0                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    13   3
  19Q LOSS WILD-TYPE 325  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     13    3
  19Q LOSS WILD-TYPE  325   72
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               13                325
  1                3                 72
[1] 2 2
[1] FALSE
D74V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0  17
  19Q LOSS WILD-TYPE  14 451
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   17
  19Q LOSS WILD-TYPE   14  451
                                        clus
vv                                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  17                451
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED     9   8   0   0
  19Q LOSS WILD-TYPE 301 130   5  15
D74V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                9                301
  R1                8                130
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, continuous
D74V8, continuous
D74V9, continuous
D74V10, continuous
D74V11, continuous
D74V12, continuous
D74V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0     3
  19Q LOSS WILD-TYPE     2                         7   143
D74V14, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    3                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = 20P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    16   1
  20P LOSS WILD-TYPE 457   7
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                17                464 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  7 
$`20P LOSS MUTATED`
TCGA-CH-5772 TCGA-EJ-5532 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7784 TCGA-FC-A4JI 
       15.98        47.87        36.13        37.81        25.68        13.45 
TCGA-G9-6339 TCGA-G9-6494 TCGA-G9-A9S0 TCGA-HC-7821 TCGA-KK-A8IJ TCGA-KK-A8IK 
       83.87        58.22        26.01        31.43        51.25        51.39 
TCGA-V1-A9Z7 TCGA-VP-A87C TCGA-YL-A8SL TCGA-ZG-A9L0 TCGA-ZG-A9LS 
        4.27        55.56        32.45        11.67        16.96 

$`20P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 
        1.02        15.06        24.03         2.04        13.02        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       41.85        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.77        28.41        15.42        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 
       30.97        35.34        28.18        32.68        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
      113.98        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        5.59         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87D TCGA-VP-A87E 
      109.58        97.41        23.93        85.18        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13         4.27        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              4.27               0.72 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             83.87             165.17 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            32.450             26.365 
[1] "4.3 - 83.9 (32.5)"  "0.7 - 165.2 (26.4)"
[1] "hr=" "4.8"
D75V2, continuous
                    vv
clus                  T2  T3  T4
  20P LOSS MUTATED     3  14   1
  20P LOSS WILD-TYPE 185 267   9
D75V3, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T2                3                185
  T3               14                267
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V4, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    10   6
  20P LOSS WILD-TYPE 328  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     10    6
  20P LOSS WILD-TYPE  328   69
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               10                328
  1                6                 69
[1] 2 2
[1] FALSE
D75V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  18
  20P LOSS WILD-TYPE  14 450
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   18
  20P LOSS WILD-TYPE   14  450
                                        clus
vv                                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  18                450
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    12   5   0   0
  20P LOSS WILD-TYPE 298 133   5  15
D75V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               12                298
  R1                5                133
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, continuous
D75V8, continuous
D75V9, continuous
D75V10, continuous
D75V11, continuous
D75V12, continuous
D75V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         1     6
  20P LOSS WILD-TYPE     2                         6   140
D75V14, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    6                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = 20Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     8   0
  20Q LOSS WILD-TYPE 465   8
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                473 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 0                  8 
$`20Q LOSS MUTATED`
TCGA-CH-5772 TCGA-EJ-5532 TCGA-EJ-7784 TCGA-FC-A4JI TCGA-G9-6494 TCGA-HC-A632 
       15.98        47.87        25.68        13.45        58.22         2.01 
TCGA-V1-A9Z7 TCGA-YL-A8SL 
        4.27        32.45 

$`20Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 
        1.02        15.06        24.03         2.04        13.02        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       41.85        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.87        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB 
        4.54         4.31         4.77        28.41        15.42        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       58.45        25.15        27.29        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.15        22.36         0.76         1.78         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       13.55        27.12        13.87         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        5.59         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       46.29       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       37.94        36.43        29.85        22.59        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       12.43         3.78        16.96        19.04        12.16        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.01               0.72 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             58.22             165.17 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             20.83              26.99 
[1] "2.0 - 58.2 (20.8)"  "0.7 - 165.2 (27.0)"
[1] "hr="     "9100000"
D76V2, continuous
                    vv
clus                  T2  T3  T4
  20Q LOSS MUTATED     1   6   1
  20Q LOSS WILD-TYPE 187 275   9
D76V3, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T2                1                187
  T3                6                275
  T4                1                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V4, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   1
  20Q LOSS WILD-TYPE 332  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    1
  20Q LOSS WILD-TYPE  332   74
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                6                332
  1                1                 74
[1] 2 2
[1] FALSE
D76V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   8
  20Q LOSS WILD-TYPE  14 460
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    8
  20Q LOSS WILD-TYPE   14  460
                                        clus
vv                                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   8                460
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     6   2   0   0
  20Q LOSS WILD-TYPE 304 136   5  15
D76V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                6                304
  R1                2                136
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, continuous
D76V8, continuous
D76V9, continuous
D76V10, continuous
D76V11, continuous
D76V12, continuous
D76V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     4
  20Q LOSS WILD-TYPE     2                         7   142
D76V14, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    4                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = 21Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    23   0
  21Q LOSS WILD-TYPE 450   8
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                23                458 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                  8 
$`21Q LOSS MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-5519 TCGA-EJ-8472 
       32.71        11.51        35.01         0.92        64.50        24.85 
TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-G9-6329 TCGA-G9-7521 TCGA-HC-7748 TCGA-HC-7821 
        8.22        15.58        41.62        30.97        26.04        31.43 
TCGA-J9-A52B TCGA-KC-A7FA TCGA-V1-A9O7 TCGA-VP-A87K TCGA-XK-AAIW TCGA-YL-A8SJ 
       13.87        19.66        79.73        42.94        40.04        45.86 
TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A9KY TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       24.33        28.34         4.27        17.98        11.47 

$`21Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 
       13.02        31.00         1.02         2.04        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       52.27        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NG 
       21.90        14.83         7.56        11.61        28.70        14.20 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 
       13.45        22.36        17.23        16.24         1.78        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 
       64.18        50.73        52.93        38.96        27.91        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57         1.48         1.68        23.70        24.59         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       13.55        27.12         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       43.66        21.86         8.65         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       58.39         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       53.06        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX 
        8.98        14.04        53.36        60.99        62.37        49.91 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC 
        3.78        16.96        19.04        12.16        22.75        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.92               0.72 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             79.73             165.17 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            26.040             26.825 
[1] "0.9 - 79.7 (26.0)"  "0.7 - 165.2 (26.8)"
[1] "hr="     "2.6e+07"
D77V2, continuous
                    vv
clus                  T2  T3  T4
  21Q LOSS MUTATED     4  16   3
  21Q LOSS WILD-TYPE 184 265   7
D77V3, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T2                4                184
  T3               16                265
  T4                3                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V4, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    13   9
  21Q LOSS WILD-TYPE 325  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     13    9
  21Q LOSS WILD-TYPE  325   66
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               13                325
  1                9                 66
[1] 2 2
[1] FALSE
D77V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  22
  21Q LOSS WILD-TYPE  13 446
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   22
  21Q LOSS WILD-TYPE   13  446
                                        clus
vv                                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  22                446
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED    11  11   0   0
  21Q LOSS WILD-TYPE 299 127   5  15
D77V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               11                299
  R1               11                127
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, continuous
D77V8, continuous
D77V9, continuous
D77V10, continuous
D77V11, continuous
D77V12, continuous
D77V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       0                         0     6
  21Q LOSS WILD-TYPE     2                         7   140
D77V14, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    6                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = 22Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    44   1
  22Q LOSS WILD-TYPE 429   7
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                436 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  7 
$`22Q LOSS MUTATED`
TCGA-2A-A8VT TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5766 TCGA-CH-5772 
       32.71        35.01         1.02         0.92         1.02        15.98 
TCGA-EJ-5511 TCGA-EJ-7783 TCGA-EJ-8472 TCGA-G9-6356 TCGA-G9-7521 TCGA-HC-7080 
       48.53        25.87        24.85        47.15        30.97        36.36 
TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A631 TCGA-HI-7168 TCGA-HI-7171 TCGA-J9-A52E 
       22.42        22.36         1.78        78.61        43.69        10.62 
TCGA-J9-A8CL TCGA-KK-A8IG TCGA-M7-A71Y TCGA-M7-A725 TCGA-V1-A8MJ TCGA-V1-A8X3 
       13.32        82.36         5.19        18.84        40.44         6.64 
TCGA-V1-A9O7 TCGA-V1-A9OL TCGA-VN-A88K TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87K 
       79.73        19.36        25.51       111.39        75.91        42.94 
TCGA-XJ-A9DX TCGA-XK-AAJA TCGA-YL-A8HM TCGA-YL-A8SB TCGA-YL-A8SQ TCGA-YL-A9WH 
       31.99        30.58        48.72        56.52        62.79        14.04 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-ZG-A8QW TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LU 
       62.37        24.33         3.09        20.28        12.43        19.04 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       17.98        14.96        11.47 

$`22Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 
        1.02        13.02        31.00         2.04        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
        1.02        23.01        15.06        24.03         2.04        13.02 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 
       23.90        38.93        48.13        36.69        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       23.90        38.37        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       77.16        76.41        38.10        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6361 
       68.68        49.81        46.16        50.70        49.35        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       50.73        52.93        38.96        27.91        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       19.76        65.26         2.93        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV 
       17.95        22.32         1.58        15.88         1.15         0.76 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 
       25.48        18.84        88.24        82.92        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CM 
       11.77        13.55        27.12        13.87         5.85        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       26.43        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       47.28        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       15.58        22.55        58.39         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       41.19        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       25.78        16.31       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-AA1N 
       55.56        60.92        66.97        21.80        53.36        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV 
       42.08        48.03         9.04         2.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        41.49        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF 
       71.77        62.14        60.56        16.83        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-YL-A9WY 
       71.34         8.98        53.36        60.99        49.91        28.34 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS 
       36.43        29.85        22.59        19.17         3.78        16.96 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        22.75        13.48         4.34 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.92               0.72 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            111.39             165.17 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            24.850             27.055 
[1] "0.9 - 111.4 (24.9)" "0.7 - 165.2 (27.1)"
[1] "hr=" "1.9"
D78V2, continuous
                    vv
clus                  T2  T3  T4
  22Q LOSS MUTATED     5  38   2
  22Q LOSS WILD-TYPE 183 243   8
D78V3, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T2                5                183
  T3               38                243
  T4                2                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V4, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    27  16
  22Q LOSS WILD-TYPE 311  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     27   16
  22Q LOSS WILD-TYPE  311   59
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               27                311
  1               16                 59
[1] 2 2
[1] FALSE
D78V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     2  43
  22Q LOSS WILD-TYPE  12 425
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   43
  22Q LOSS WILD-TYPE   12  425
                                        clus
vv                                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                2                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  43                425
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    21  24   0   0
  22Q LOSS WILD-TYPE 289 114   5  15
D78V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               21                289
  R1               24                114
  R2                0                  5
  RX                0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, continuous
D78V8, continuous
D78V9, continuous
D78V10, continuous
D78V11, continuous
D78V12, continuous
D78V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       0                         1    10
  22Q LOSS WILD-TYPE     2                         6   136
D78V14, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   10                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = XP LOSS MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    36   1
  XP LOSS WILD-TYPE 437   7
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               37               444 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                1                 7 
$`XP LOSS MUTATED`
TCGA-CH-5753 TCGA-EJ-5507 TCGA-EJ-7312 TCGA-EJ-7783 TCGA-EJ-7789 TCGA-EJ-A65D 
        1.02        23.90        36.13        25.87        18.15        12.92 
TCGA-G9-6369 TCGA-G9-6499 TCGA-HC-7213 TCGA-HC-A48F TCGA-HC-A8CY TCGA-HI-7171 
       39.95        50.73        40.08        22.36         9.53        43.69 
TCGA-J4-A67N TCGA-J9-A8CL TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 
       16.54        13.32        56.28        86.40        30.02        54.54 
TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A8IH TCGA-TP-A8TV TCGA-V1-A9O5 TCGA-V1-A9O9 
      113.33        58.19        66.18        13.32        58.39         6.71 
TCGA-VN-A943 TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XK-AAJP TCGA-YL-A8SC 
       16.31        42.94        44.88        14.76        41.39        41.46 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A9WL TCGA-ZG-A9KY TCGA-ZG-A9LM TCGA-ZG-A9M4 
       46.29        32.45        24.33         4.27        12.43        17.98 
TCGA-ZG-A9ND 
       13.48 

$`XP LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 
       24.03         1.02        13.02        35.01        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       26.30        45.73        28.93        30.31        27.19        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
       25.68        20.55        14.53        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F 
       21.96        23.80        21.96        23.34        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 
       39.39        44.81         3.32        40.18        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
        1.58        15.88         1.15         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         7.00         4.93        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       78.61        88.24        82.92        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       25.32        30.94        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN 
       27.12        13.87         5.85        10.62        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       44.68       115.86       165.17        67.59       115.13        49.25 
TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       67.07         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       82.36       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG 
      122.17        86.14        18.12        11.90        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9OA 
       30.38        15.58        22.55         6.64        79.73        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       66.97        21.80        53.36        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        56.52        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       45.86       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        60.99        62.37        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS 
       29.85        22.59        20.28        19.17         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       19.04        12.16        22.75        14.96        11.47         4.34 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             1.02              0.72 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           113.33            165.17 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           30.020            26.545 
[1] "1.0 - 113.3 (30.0)" "0.7 - 165.2 (26.5)"
[1] "hr=" "2.4"
D79V2, continuous
                   vv
clus                 T2  T3  T4
  XP LOSS MUTATED     7  28   2
  XP LOSS WILD-TYPE 181 253   8
D79V3, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T2               7               181
  T3              28               253
  T4               2                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V4, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    24  12
  XP LOSS WILD-TYPE 314  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     24   12
  XP LOSS WILD-TYPE  314   63
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              24               314
  1              12                63
[1] 2 2
[1] FALSE
D79V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2  35
  XP LOSS WILD-TYPE  12 433
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   35
  XP LOSS WILD-TYPE   12  433
                                        clus
vv                                       XP LOSS MUTATED XP LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               2                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 35               433
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    22  13   0   2
  XP LOSS WILD-TYPE 288 125   5  13
D79V6, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              22               288
  R1              13               125
  R2               0                 5
  RX               2                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, continuous
D79V8, continuous
D79V9, continuous
D79V10, continuous
D79V11, continuous
D79V12, continuous
D79V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       0                         1     7
  XP LOSS WILD-TYPE     2                         6   139
D79V14, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   7               139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    36   1
  XQ LOSS WILD-TYPE 437   7
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               37               444 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                 7 
$`XQ LOSS MUTATED`
TCGA-CH-5753 TCGA-EJ-5507 TCGA-EJ-7312 TCGA-EJ-7783 TCGA-EJ-7789 TCGA-EJ-A65D 
        1.02        23.90        36.13        25.87        18.15        12.92 
TCGA-G9-6369 TCGA-G9-6499 TCGA-HC-7213 TCGA-HC-A48F TCGA-HC-A8CY TCGA-HI-7171 
       39.95        50.73        40.08        22.36         9.53        43.69 
TCGA-J4-A67N TCGA-J9-A8CL TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 
       16.54        13.32        56.28        86.40        30.02        54.54 
TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A8IH TCGA-TP-A8TV TCGA-V1-A9O5 TCGA-V1-A9O9 
      113.33        58.19        66.18        13.32        58.39         6.71 
TCGA-VN-A943 TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XK-AAJP TCGA-YL-A8SC 
       16.31        42.94        44.88        14.76        41.39        41.46 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A9WL TCGA-ZG-A9KY TCGA-ZG-A9LM TCGA-ZG-A9M4 
       46.29        32.45        24.33         4.27        12.43        17.98 
TCGA-ZG-A9ND 
       13.48 

$`XQ LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 
       24.03         1.02        13.02        35.01        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       26.30        45.73        28.93        30.31        27.19        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
       25.68        20.55        14.53        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F 
       21.96        23.80        21.96        23.34        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 
       39.39        44.81         3.32        40.18        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
        1.58        15.88         1.15         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         7.00         4.93        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       78.61        88.24        82.92        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       25.32        30.94        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN 
       27.12        13.87         5.85        10.62        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       44.68       115.86       165.17        67.59       115.13        49.25 
TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       67.07         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       82.36       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG 
      122.17        86.14        18.12        11.90        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9OA 
       30.38        15.58        22.55         6.64        79.73        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       66.97        21.80        53.36        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        56.52        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       45.86       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        60.99        62.37        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS 
       29.85        22.59        20.28        19.17         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       19.04        12.16        22.75        14.96        11.47         4.34 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             1.02              0.72 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           113.33            165.17 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           30.020            26.545 
[1] "1.0 - 113.3 (30.0)" "0.7 - 165.2 (26.5)"
[1] "hr=" "2.4"
D80V2, continuous
                   vv
clus                 T2  T3  T4
  XQ LOSS MUTATED     7  28   2
  XQ LOSS WILD-TYPE 181 253   8
D80V3, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T2               7               181
  T3              28               253
  T4               2                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V4, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    24  12
  XQ LOSS WILD-TYPE 314  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     24   12
  XQ LOSS WILD-TYPE  314   63
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              24               314
  1              12                63
[1] 2 2
[1] FALSE
D80V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  35
  XQ LOSS WILD-TYPE  12 433
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   35
  XQ LOSS WILD-TYPE   12  433
                                        clus
vv                                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               2                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 35               433
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    22  13   0   2
  XQ LOSS WILD-TYPE 288 125   5  13
D80V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              22               288
  R1              13               125
  R2               0                 5
  RX               2                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, continuous
D80V8, continuous
D80V9, continuous
D80V10, continuous
D80V11, continuous
D80V12, continuous
D80V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       0                         1     7
  XQ LOSS WILD-TYPE     2                         6   139
D80V14, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   7               139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
