[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/22506989/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/22533740/transformed.cor.cli.txt"

nPatients in clinical file=499, in cluster file=492, common to both=492
[1] "Reduce the number of clustering variables from 82 to 80."
[1]  80 492
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               15               477 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               15               477 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26               466 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26               466 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               481 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               481 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7               485 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7               485 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               40               452 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               40               452 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               54               438 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               54               438 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               483 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               483 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               482 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               482 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23               469 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23               469 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               480 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               480 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               482 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               482 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               486 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               486 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              101               391 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              101               391 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               94               398 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               94               398 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               68               424 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               68               424 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              126               366 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              126               366 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               34               458 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               34               458 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               48               444 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               48               444 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                15                477 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                15                477 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                478 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                478 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                465 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                465 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                30                462 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                30                462 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                477 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                477 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                474 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                474 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                484 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                484 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                10                482 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                10                482 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                486 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                486 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                32                460 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                32                460 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                485 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                485 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                484 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                484 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                11                481 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                11                481 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                19                473 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                19                473 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                482 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                482 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                12                480 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                12                480 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                12                480 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                12                480 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                26                466 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                26                466 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                29                463 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                29                463 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                471 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                471 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                488 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                488 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7               485 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7               485 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               485 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               485 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               22               470 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               22               470 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6               486 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6               486 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               478 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               478 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               474 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               474 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9               483 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9               483 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5               487 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5               487 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               469 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               469 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16               476 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16               476 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12               480 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12               480 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23               469 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23               469 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               26               466 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               26               466 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               41               451 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               41               451 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              171               321 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              171               321 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               471 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               471 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               21               471 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               21               471 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               481 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               481 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                41                451 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                41                451 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                43                449 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                43                449 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                484 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                484 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                487 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                487 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                47                445 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                47                445 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                472 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                472 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                78                414 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                78                414 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                467 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                467 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                35                457 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                35                457 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                31                461 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                31                461 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               107                385 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               107                385 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                76                416 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                76                416 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                20                472 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                20                472 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                425 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                425 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               100                392 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               100                392 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                473 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                473 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                18                474 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                18                474 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                473 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                473 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                484 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                484 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                24                468 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                24                468 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                47                445 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                47                445 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               38               454 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               38               454 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               38               454 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               38               454 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "GLEASON_SCORE"                       
[17] "PSA_VALUE"                           
[18] "DAYS_TO_PSA"                         
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 492 columns.

[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=9,	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=431,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE 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:'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 11:'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 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'PSA_VALUE':	nDistinctValues=92,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'DAYS_TO_PSA':	nDistinctValues=379,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'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)"
[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 492 columns, 1 survival variables, and 10 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"     "PATHOLOGY_N_STAGE"    
 [4] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
 [7] "NUMBER_OF_LYMPH_NODES" "GLEASON_SCORE"         "PSA_VALUE"            
[10] "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 
187 288  10 
[1] "table(vv)"
vv
 T2  T3  T4 
187 288  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T2  T3  T4 
187 288  10 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
187 288  10 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=11, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=92, 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    15   0
  1P GAIN WILD-TYPE 468   9
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               15               477 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                 9 
$`1P GAIN MUTATED`
TCGA-CH-5766 TCGA-EJ-5518 TCGA-EJ-7788 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6499 
        1.02        69.63        28.24        15.42        28.83        50.73 
TCGA-J4-AATZ TCGA-J9-A52E TCGA-J9-A8CM TCGA-V1-A9O7 TCGA-VP-A875 TCGA-XK-AAIV 
       13.55        10.62        15.22        82.16        75.91        37.25 
TCGA-YL-A8HM TCGA-YL-A8SR TCGA-ZG-A9L5 
       48.72         8.98        29.85 

$`1P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 
        2.04         0.92        44.02        23.01        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 
       60.13        60.23        62.10        62.10        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       38.70        36.03        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
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-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
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-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        4.77        28.41        22.36        17.23        25.94        20.25 
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        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        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 
       35.44        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CP 
       27.12        13.87         5.85        10.55        13.32        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        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        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        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
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-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       61.68        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        63.52        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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 
       75.75        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        77.79        68.48        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       13.28        10.13         4.27        11.67        42.81        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              0.76 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            82.16            165.17 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            28.83             30.81 
[1] "1.0 - 82.2 (28.8)"  "0.8 - 165.2 (30.8)"
[1] "hr="     "9400000"
D1V2, continuous
                   vv
clus                 T2  T3  T4
  1P GAIN MUTATED     0  13   2
  1P GAIN WILD-TYPE 187 275   8
D1V3, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T2               0               187
  T3              13               275
  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"
D1V4, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    10   4
  1P GAIN WILD-TYPE 333  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     10    4
  1P GAIN WILD-TYPE  333   73
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              10               333
  1               4                73
[1] 2 2
[1] FALSE
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     9   5
  1P GAIN WILD-TYPE 381  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      9    5
  1P GAIN WILD-TYPE  381   54
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                9               381
  YES               5                54
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    15   0
  1P GAIN WILD-TYPE 463  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     15    0
  1P GAIN WILD-TYPE  463   14
                                        clus
vv                                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 15               463
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED     6   8   0   0
  1P GAIN WILD-TYPE 307 136   5  15
D1V7, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               6               307
  R1               8               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"
D1V8, continuous
D1V9, continuous
D1V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         0     5
  1P GAIN WILD-TYPE     2                         7   141
D1V11, 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    26   0
  1Q GAIN WILD-TYPE 457   9
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26               466 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 9 
$`1Q GAIN MUTATED`
TCGA-CH-5766 TCGA-EJ-5518 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-FC-7961 TCGA-FC-A4JI 
        1.02        69.63        25.68        28.24        15.42        28.83 
TCGA-G9-6362 TCGA-G9-6499 TCGA-HI-7168 TCGA-J4-AATZ TCGA-J9-A52E TCGA-J9-A8CM 
       47.44        50.73       109.25        13.55        10.62        15.22 
TCGA-KK-A8I4 TCGA-M7-A725 TCGA-V1-A8WW TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-VN-A88K 
       74.27        18.84        35.44        63.52        82.16        25.51 
TCGA-VN-A88Q TCGA-VP-A875 TCGA-XK-AAIV TCGA-YL-A8HM TCGA-YL-A8SR TCGA-ZG-A9L5 
       44.91        75.91        37.25        48.72         8.98        29.85 
TCGA-ZG-A9LZ TCGA-ZG-A9NI 
       22.75         4.34 

$`1Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 
        2.04         0.92        44.02        23.01        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 
       60.13        60.23        62.10        62.10        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        38.70 
TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       36.03        36.33        45.90         3.75        42.94        32.32 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       77.16        76.41        38.10        24.85        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         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-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.41        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.15        46.52        45.30        44.81        64.01        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-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 
       25.48        18.84        19.30        27.75        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        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        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-AATV TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       23.67        17.85        18.18        27.12        13.87         5.85 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       10.55        13.32        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        83.34        64.70        86.40       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       90.74        58.19        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-A8I5 
       57.67        49.94        43.69        34.95        36.13       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
       21.96        65.82        31.79        32.91        63.48        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 
       67.46        20.65        62.96        16.21        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
        6.64        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         8.84 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R 
       24.53         6.21        25.18        15.81        41.42        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       16.31       119.38       109.58       102.90        23.93        89.49 
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        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        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-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         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        75.75        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        77.79        68.48 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        42.81        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-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       17.98        14.96        11.47        13.48 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.02              0.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           109.25            165.17 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            29.34             30.76 
[1] "1.0 - 109.2 (29.3)" "0.8 - 165.2 (30.8)"
[1] "hr="     "2.7e+07"
D2V2, continuous
                   vv
clus                 T2  T3  T4
  1Q GAIN MUTATED     2  21   3
  1Q GAIN WILD-TYPE 185 267   7
D2V3, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T2               2               185
  T3              21               267
  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   8
  1Q GAIN WILD-TYPE 326  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17    8
  1Q GAIN WILD-TYPE  326   69
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              17               326
  1               8                69
[1] 2 2
[1] FALSE
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    18   7
  1Q GAIN WILD-TYPE 372  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     18    7
  1Q GAIN WILD-TYPE  372   52
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               18               372
  YES               7                52
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    25   1
  1Q GAIN WILD-TYPE 453  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     25    1
  1Q GAIN WILD-TYPE  453   13
                                        clus
vv                                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 25               453
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               1                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    12  13   0   0
  1Q GAIN WILD-TYPE 301 131   5  15
D2V7, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              12               301
  R1              13               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"
D2V8, continuous
D2V9, continuous
D2V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       0                         0     8
  1Q GAIN WILD-TYPE     2                         7   138
D2V11, 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    11   0
  2P GAIN WILD-TYPE 472   9
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               481 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                0                 9 
$`2P GAIN MUTATED`
TCGA-4L-AA1F TCGA-EJ-A65M TCGA-FC-A4JI TCGA-HC-8256 TCGA-HC-A631 TCGA-HC-A9TE 
       11.51         7.56        28.83        28.27         1.78        19.30 
TCGA-KK-A8IF TCGA-KK-A8IK TCGA-YL-A8S8 TCGA-YL-A8SQ TCGA-ZG-A9LN 
       26.43        67.46        62.14        68.48         3.78 

$`2P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 
        3.68        28.37        44.84        41.82        20.22         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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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 
       25.94        20.25        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        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87        27.85        30.38        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        15.55        22.36         0.76         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH 
        4.41         4.93         9.53        25.48        18.84        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK 
       13.55        27.12        13.87         5.85        10.62        10.55 
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        83.34        64.70        86.40       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       90.74        58.19        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-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
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-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        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       35.44         6.64        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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 
       25.18        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 
      119.38        75.91       109.58       102.90        23.93        89.49 
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        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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        75.75 
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        77.79 
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        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU 
       22.59        20.28        19.17        12.43        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 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.78              0.76 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            68.48            165.17 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            26.43             30.84 
[1] "1.8 - 68.5 (26.4)"  "0.8 - 165.2 (30.8)"
[1] "hr="     "9200000"
D3V2, continuous
                   vv
clus                 T2  T3  T4
  2P GAIN MUTATED     4   7   0
  2P GAIN WILD-TYPE 183 281  10
D3V3, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T2               4               183
  T3               7               281
  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     8   1
  2P GAIN WILD-TYPE 335  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8    1
  2P GAIN WILD-TYPE  335   76
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               8               335
  1               1                76
[1] 2 2
[1] FALSE
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     8   1
  2P GAIN WILD-TYPE 382  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8    1
  2P GAIN WILD-TYPE  382   58
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                8               382
  YES               1                58
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    11   0
  2P GAIN WILD-TYPE 467  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     11    0
  2P GAIN WILD-TYPE  467   14
                                        clus
vv                                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 11               467
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED     4   6   0   0
  2P GAIN WILD-TYPE 309 138   5  15
D3V7, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               4               309
  R1               6               138
  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"
D3V8, continuous
D3V9, continuous
D3V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0     0
  2P GAIN WILD-TYPE     2                         7   146
D3V11, multiclass

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED     7   0
  2Q GAIN WILD-TYPE 476   9
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7               485 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                0                 9 
$`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        28.83         1.78        26.43        68.48 
TCGA-ZG-A9LN 
        3.78 

$`2Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 
        3.68        28.37        44.84        41.82        20.22         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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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 
       25.94        20.25        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        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        22.36         0.76 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       19.30        27.75       109.25        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        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        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        83.34        64.70        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        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        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH 
       32.91        63.48        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        67.46        20.65        62.96        16.21 
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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 
       30.38        15.58        22.55        35.44         6.64        63.52 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       82.16        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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        75.75        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        77.79         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        70.22        24.33        49.91        36.10 
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-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       19.17        12.43        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 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.78              0.76 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            68.48            165.17 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            11.51             30.84 
[1] "1.8 - 68.5 (11.5)"  "0.8 - 165.2 (30.8)"
[1] "hr="     "3300000"
D4V2, continuous
                   vv
clus                 T2  T3  T4
  2Q GAIN MUTATED     2   5   0
  2Q GAIN WILD-TYPE 185 283  10
D4V3, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T2               2               185
  T3               5               283
  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 338  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5    1
  2Q GAIN WILD-TYPE  338   76
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               5               338
  1               1                76
[1] 2 2
[1] FALSE
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     4   1
  2Q GAIN WILD-TYPE 386  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    1
  2Q GAIN WILD-TYPE  386   58
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                4               386
  YES               1                58
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     7   0
  2Q GAIN WILD-TYPE 471  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      7    0
  2Q GAIN WILD-TYPE  471   14
                                        clus
vv                                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  7               471
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED     2   4   0   0
  2Q GAIN WILD-TYPE 311 140   5  15
D4V7, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               2               311
  R1               4               140
  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"
D4V8, continuous
D4V9, continuous
D4V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0     0
  2Q GAIN WILD-TYPE     2                         7   146
D4V11, multiclass

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    38   2
  3P GAIN WILD-TYPE 445   7
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               40               452 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                 7 
$`3P GAIN MUTATED`
TCGA-CH-5791 TCGA-HC-A76W TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-CH-5751 TCGA-CH-5761 
       33.01         7.00        32.45         2.73        35.01         0.92 
TCGA-CH-5771 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5531 TCGA-EJ-7782 TCGA-EJ-7792 
       13.02        60.13        69.63        41.85        38.37        45.90 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6499 TCGA-G9-A9S0 TCGA-HC-8216 TCGA-HC-A631 
       15.42        28.83        50.73        26.01        22.42         1.78 
TCGA-HC-A6AS TCGA-HC-A9TE TCGA-HI-7168 TCGA-KK-A8IA TCGA-KK-A8IF TCGA-KK-A8II 
        1.45        19.30       109.25        63.48        26.43       113.98 
TCGA-KK-A8IK TCGA-V1-A8WW TCGA-VP-A872 TCGA-VP-A87H TCGA-XJ-A83G TCGA-XK-AAIV 
       67.46        35.44       119.38        21.80        48.03        37.25 
TCGA-YJ-A8SW TCGA-YL-A8S8 TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A9L0 TCGA-ZG-A9L5 
        4.87        62.14        14.04        53.36        11.67        29.85 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LS TCGA-ZG-A9LZ 
       20.28        19.17        16.96        22.75 

$`3P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-EJ-5542 
        1.02        12.00         1.02        15.98        32.02        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 
        3.48        32.61        40.67        19.66         6.44        29.56 
TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT 
       41.00        41.49        32.19        20.42        55.92        45.14 
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        45.30         3.68        28.37        44.84        41.82 
TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 
       20.22        11.51         2.99         6.97        22.06         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       12.99        13.97         1.97        24.03         1.02        13.02 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       31.00         2.04        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
       24.03         2.04        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       60.23        62.10        62.10        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5532 
       61.87        36.66        62.76        58.45        60.23        60.10 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       88.34        93.70        83.57        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       33.83        27.09        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 
       35.28        25.87        25.68        38.70        36.03        28.24 
TCGA-EJ-7789 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       36.33         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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-A5OB 
        8.75         4.54         4.31         4.77        28.41        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        28.18        32.68 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        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 
       27.85        30.38        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        15.55        22.36         0.76         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
        1.61        17.42         2.33         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        27.75        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        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
        5.85        10.62        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        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        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       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        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        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        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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 
       25.18        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58       102.90        23.93        89.49        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       60.92        66.97        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI 
       45.47        32.19        12.36        37.05        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       32.61        17.29        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       75.75        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 
       77.79        68.48         8.98        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LM 
        4.27        42.81        37.94        36.43        22.59        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
        3.78        19.04        12.16        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.92              0.76 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           119.38            165.17 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            29.34             30.76 
[1] "0.9 - 119.4 (29.3)" "0.8 - 165.2 (30.8)"
[1] "hr=" "2.4"
D5V2, continuous
                   vv
clus                 T2  T3  T4
  3P GAIN MUTATED     7  30   3
  3P GAIN WILD-TYPE 180 258   7
D5V3, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T2               7               180
  T3              30               258
  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    27  12
  3P GAIN WILD-TYPE 316  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     27   12
  3P GAIN WILD-TYPE  316   65
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              27               316
  1              12                65
[1] 2 2
[1] FALSE
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    26   7
  3P GAIN WILD-TYPE 364  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26    7
  3P GAIN WILD-TYPE  364   52
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               26               364
  YES               7                52
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    37   3
  3P GAIN WILD-TYPE 441  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     37    3
  3P GAIN WILD-TYPE  441   11
                                        clus
vv                                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 37               441
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               3                11
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    18  18   1   1
  3P GAIN WILD-TYPE 295 126   4  14
D5V7, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              18               295
  R1              18               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"
D5V8, continuous
D5V9, continuous
D5V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         1    11
  3P GAIN WILD-TYPE     2                         6   135
D5V11, 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    51   3
  3Q GAIN WILD-TYPE 432   6
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               54               438 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                 6 
$`3Q GAIN MUTATED`
TCGA-CH-5791 TCGA-EJ-A65J TCGA-HC-A76W TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB 
       33.01        14.83         7.00        29.56        32.45         2.73 
TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5771 TCGA-CH-5788 TCGA-EJ-5514 TCGA-EJ-5518 
       11.51        35.01        13.02        26.99        60.13        69.63 
TCGA-EJ-5521 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7782 TCGA-EJ-7792 TCGA-FC-7961 
       74.93        58.45        41.85        38.37        45.90        15.42 
TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6363 TCGA-G9-6499 TCGA-G9-A9S0 TCGA-HC-8216 
       28.83        66.67        45.30        50.73        26.01        22.42 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AS TCGA-HC-A8CY TCGA-HC-A9TE TCGA-HI-7168 
        0.76         1.78         1.45         9.53        19.30       109.25 
TCGA-J4-AATZ TCGA-KK-A6E1 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8II 
       13.55        72.26        63.48        67.43        26.43       113.98 
TCGA-KK-A8IK TCGA-V1-A8WW TCGA-VP-A872 TCGA-VP-A87H TCGA-XJ-A83G TCGA-XK-AAIV 
       67.46        35.44       119.38        21.80        48.03        37.25 
TCGA-YJ-A8SW TCGA-YL-A8S8 TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
        4.87        62.14        77.79        14.04        53.36        60.99 
TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LZ TCGA-ZG-A9MC 
       11.67        29.85        20.28        19.17        22.75        14.96 

$`3Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-EJ-5542 
        1.02        12.00         1.02        15.98        32.02        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ 
       28.70        39.39        44.55        26.04        31.43         3.48 
TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-QU-A6IM TCGA-XK-AAJ3 
       32.61        40.67        19.66         6.44        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 
        3.68        28.37        44.84        41.82        20.22         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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
        9.99         2.99        29.00        48.56        57.86        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       46.92        30.31        45.40        47.90        64.60        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       62.04        48.53        56.98        60.23        62.10        62.10 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 
       64.50        68.35        61.87        36.66        62.76        60.23 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        35.28        25.87        25.68        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       28.24        36.33         3.75        42.94        32.32        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       18.41        21.90         7.56        11.61         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        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       47.44        44.81        64.01        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-A9S7 
       27.91        30.97        35.44        28.18        32.68        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        17.16        25.71        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        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       15.55        22.36         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 
        2.33         1.25         4.41         4.93        25.48        18.84 
TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       27.75        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       27.12        13.87         5.85        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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-A6E2 
       83.34        64.70        86.40       141.21        48.76       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH 
       65.82        31.79        32.91        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        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        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        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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 
       25.18        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58       102.90        23.93        89.49        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       60.92        66.97        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI 
       45.47        32.19        12.36        37.05        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       32.61        17.29        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       75.75        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-A8SQ TCGA-YL-A8SR TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       68.48         8.98        70.22        24.33        49.91        36.10 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L1 
        3.09        14.53        13.28        10.13         4.27        42.81 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       37.94        36.43        22.59        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       19.04        12.16        17.98        11.47        13.48         4.34 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.76              0.89 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           119.38            165.17 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           31.150            30.645 
[1] "0.8 - 119.4 (31.2)" "0.9 - 165.2 (30.6)"
[1] "hr=" "3.1"
D6V2, continuous
                   vv
clus                 T2  T3  T4
  3Q GAIN MUTATED     7  43   4
  3Q GAIN WILD-TYPE 180 245   6
D6V3, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T2               7               180
  T3              43               245
  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  16
  3Q GAIN WILD-TYPE 307  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     36   16
  3Q GAIN WILD-TYPE  307   61
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              36               307
  1              16                61
[1] 2 2
[1] FALSE
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    36  10
  3Q GAIN WILD-TYPE 354  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     36   10
  3Q GAIN WILD-TYPE  354   49
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               36               354
  YES              10                49
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    51   3
  3Q GAIN WILD-TYPE 427  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     51    3
  3Q GAIN WILD-TYPE  427   11
                                        clus
vv                                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 51               427
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               3                11
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    24  25   1   2
  3Q GAIN WILD-TYPE 289 119   4  13
D6V7, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              24               289
  R1              25               119
  R2               1                 4
  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"
D6V8, continuous
D6V9, continuous
D6V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         1    15
  3Q GAIN WILD-TYPE     2                         6   131
D6V11, 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     9   0
  4P GAIN WILD-TYPE 474   9
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               483 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                 9 
$`4P GAIN MUTATED`
TCGA-EJ-5542 TCGA-G9-6499 TCGA-HC-7080 TCGA-HC-A9TE TCGA-KK-A8I4 TCGA-VP-A875 
       49.74        50.73        36.36        19.30        74.27        75.91 
TCGA-YL-A8HO TCGA-YL-A8SR TCGA-ZG-A9LY 
       75.75         8.98        12.16 

$`4P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 
       19.76        69.53        65.26        38.93        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-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-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       18.84        27.75       109.25        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        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        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        83.34        64.70        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        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        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       36.13       101.79        21.96        65.82        31.79        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-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        67.46        20.65        62.96        16.21 
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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 
       30.38        15.58        22.55        35.44         6.64        63.52 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       82.16        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         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        25.18        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       119.38       109.58       102.90 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        89.49        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 
       58.32        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 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA 
        2.99        31.99        31.96        37.25        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        77.79        68.48        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       13.28        10.13         4.27        11.67        42.81        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-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
        3.78        16.96        19.04        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             8.98              0.76 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            75.91            165.17 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            49.74             30.51 
[1] "9.0 - 75.9 (49.7)"  "0.8 - 165.2 (30.5)"
[1] "hr="     "9300000"
D7V2, continuous
                   vv
clus                 T2  T3  T4
  4P GAIN MUTATED     1   8   0
  4P GAIN WILD-TYPE 186 280  10
D7V3, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T2               1               186
  T3               8               280
  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     7   2
  4P GAIN WILD-TYPE 336  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      7    2
  4P GAIN WILD-TYPE  336   75
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               7               336
  1               2                75
[1] 2 2
[1] FALSE
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     8   1
  4P GAIN WILD-TYPE 382  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8    1
  4P GAIN WILD-TYPE  382   58
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                8               382
  YES               1                58
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     9   0
  4P GAIN WILD-TYPE 469  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      9    0
  4P GAIN WILD-TYPE  469   14
                                        clus
vv                                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  9               469
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     5   4   0   0
  4P GAIN WILD-TYPE 308 140   5  15
D7V7, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               5               308
  R1               4               140
  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"
D7V8, continuous
D7V9, continuous
D7V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         0     3
  4P GAIN WILD-TYPE     2                         7   143
D7V11, 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 473   9
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               482 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                 9 
$`4Q GAIN MUTATED`
TCGA-EJ-5542 TCGA-HC-7080 TCGA-KK-A8I4 TCGA-V1-A8WV TCGA-VP-A875 TCGA-XK-AAJT 
       49.74        36.36        74.27        22.55        75.91        47.15 
TCGA-YJ-A8SW TCGA-YL-A8HO TCGA-ZG-A9LS TCGA-ZG-A9LY 
        4.87        75.75        16.96        12.16 

$`4Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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        35.44 
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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 
        3.68        19.76        69.53        65.26        38.93        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        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        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85        10.62        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       43.69        34.95        36.13       101.79        21.96        65.82 
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-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 
       61.68        64.04        30.38        15.58        35.44         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       30.58        41.39        36.95        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       32.61        17.29        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-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       77.79        68.48         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 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       13.28        10.13         4.27        11.67        42.81        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-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
        3.78        19.04        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             4.87              0.76 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            75.91            165.17 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           41.755            30.545 
[1] "4.9 - 75.9 (41.8)"  "0.8 - 165.2 (30.5)"
[1] "hr="     "9300000"
D8V2, continuous
                   vv
clus                 T2  T3  T4
  4Q GAIN MUTATED     1   9   0
  4Q GAIN WILD-TYPE 186 279  10
D8V3, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T2               1               186
  T3               9               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"
D8V4, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     6   4
  4Q GAIN WILD-TYPE 337  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      6    4
  4Q GAIN WILD-TYPE  337   73
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               6               337
  1               4                73
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7   2
  4Q GAIN WILD-TYPE 383  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    2
  4Q GAIN WILD-TYPE  383   57
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                7               383
  YES               2                57
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     9   1
  4Q GAIN WILD-TYPE 469  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      9    1
  4Q GAIN WILD-TYPE  469   13
                                        clus
vv                                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  9               469
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               1                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     5   5   0   0
  4Q GAIN WILD-TYPE 308 139   5  15
D8V7, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               5               308
  R1               5               139
  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"
D8V8, continuous
D8V9, continuous
D8V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         0     2
  4Q GAIN WILD-TYPE     2                         7   144
D8V11, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               153 
       TCGA-CH-5753        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-EJ-7123        TCGA-EJ-7791 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748        TCGA-HC-7821 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       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-5754        TCGA-CH-5761        TCGA-CH-5762        TCGA-CH-5765 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5771        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5792 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5532        TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7314 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        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-G9-6365 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075        TCGA-HC-7077 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7081        TCGA-HC-7209 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7736 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7749 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7820        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 460   9
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23               469 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                0                 9 
$`5P GAIN MUTATED`
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-CH-5761 TCGA-EJ-5495 TCGA-FC-A4JI TCGA-HC-A4ZV 
       32.45         2.73         0.92        57.86        28.83         0.76 
TCGA-J9-A52E TCGA-KK-A8IA TCGA-KK-A8IF TCGA-KK-A8IK TCGA-V1-A9O5 TCGA-VP-A872 
       10.62        63.48        26.43        67.46        63.52       119.38 
TCGA-VP-A875 TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8SL TCGA-YL-A9WH 
       75.91        21.80        37.25        75.75        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-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
        6.44        29.56        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        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-5762 
        1.02        13.02        35.01        31.00         2.04        44.02 
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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 
       26.99         9.99         2.99        29.00        48.56        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       46.92        30.31        45.40        47.90        64.60        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       62.04        48.53        56.98        60.13        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        69.63        64.50        74.93        68.35        61.87 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        62.76        58.45        60.23        41.85        60.10 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       88.34        93.70        83.57        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       33.83        27.09        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 
       35.28        38.37        25.87        25.68        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       28.24        36.33        45.90         3.75        42.94        32.32 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       77.16        76.41        38.10        24.85        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         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        25.94        20.25 
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        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        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        35.44        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        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 
       27.85        30.38        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
       15.88        15.55        22.36         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CL 
       13.55        27.12        13.87         5.85        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID 
       21.96        65.82        31.79        32.91        67.43        69.27 
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        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 
       64.04        30.38        15.58        22.55        35.44         6.64 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       82.16        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         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        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       44.91        25.78        16.31       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       89.49        55.56        60.92        66.97        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        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-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         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-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        46.29       114.38        77.79        68.48         8.98 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        70.22        24.33        49.91        36.10 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9L2 
        3.09        14.53        13.28         4.27        42.81        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-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 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.76              0.89 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           119.38            165.17 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            28.83             30.81 
[1] "0.8 - 119.4 (28.8)" "0.9 - 165.2 (30.8)"
[1] "hr="     "7.7e+07"
D9V2, continuous
                   vv
clus                 T2  T3  T4
  5P GAIN MUTATED     1  20   2
  5P GAIN WILD-TYPE 186 268   8
D9V3, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T2               1               186
  T3              20               268
  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 331  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     12   10
  5P GAIN WILD-TYPE  331   67
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              12               331
  1              10                67
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    13   6
  5P GAIN WILD-TYPE 377  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     13    6
  5P GAIN WILD-TYPE  377   53
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               13               377
  YES               6                53
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    22   1
  5P GAIN WILD-TYPE 456  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     22    1
  5P GAIN WILD-TYPE  456   13
                                        clus
vv                                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 22               456
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               1                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED     9  12   1   1
  5P GAIN WILD-TYPE 304 132   4  14
D9V7, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0               9               304
  R1              12               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"
D9V8, continuous
D9V9, continuous
D9V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       0                         0     2
  5P GAIN WILD-TYPE     2                         7   144
D9V11, multiclass
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2               153 
       TCGA-CH-5753        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-EJ-5542        TCGA-EJ-7123 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7791        TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5752        TCGA-CH-5754        TCGA-CH-5762        TCGA-CH-5765 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5771        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5792 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5496        TCGA-EJ-5497 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7788        TCGA-EJ-7789        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-G9-6365        TCGA-G9-6366 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7736 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7749 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7820        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 471   9
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               480 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                 9 
$`5Q GAIN MUTATED`
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-EJ-5495 TCGA-J9-A52E TCGA-J9-A8CL TCGA-KK-A8IA 
       32.45         2.73        57.86        10.62        13.32        63.48 
TCGA-VP-A875 TCGA-VP-A87H TCGA-YL-A8HO TCGA-YL-A8SL TCGA-ZG-A8QZ TCGA-ZG-A9L0 
       75.91        21.80        75.75        32.45        10.13        11.67 

$`5Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
        6.44        29.56        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        56.55        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        46.92        30.31        45.40        47.90        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        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        35.28        38.37        25.87        25.68        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
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-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
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        28.83        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       25.94        20.25        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        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        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        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
        5.85        10.55        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-A7FD 
       19.96        44.35        43.66        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        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        32.91 
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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       89.49        55.56        60.92        66.97        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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-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        77.79        68.48 
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        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9KY 
       49.91        36.10         3.09        14.53        13.28         4.27 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        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 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2.73              0.76 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            75.91            165.17 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           27.125            30.645 
[1] "2.7 - 75.9 (27.1)"  "0.8 - 165.2 (30.6)"
[1] "hr="     "9300000"
D10V2, continuous
                   vv
clus                 T2  T3  T4
  5Q GAIN MUTATED     0  12   0
  5Q GAIN WILD-TYPE 187 276  10
D10V3, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T2               0               187
  T3              12               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"
D10V4, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     5   6
  5Q GAIN WILD-TYPE 338  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5    6
  5Q GAIN WILD-TYPE  338   71
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               5               338
  1               6                71
[1] 2 2
[1] FALSE
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     9   1
  5Q GAIN WILD-TYPE 381  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      9    1
  5Q GAIN WILD-TYPE  381   58
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                9               381
  YES               1                58
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    12   0
  5Q GAIN WILD-TYPE 466  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     12    0
  5Q GAIN WILD-TYPE  466   14
                                        clus
vv                                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 12               466
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED     4   6   1   1
  5Q GAIN WILD-TYPE 309 138   4  14
D10V7, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0               4               309
  R1               6               138
  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"
D10V8, continuous
D10V9, continuous
D10V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         0     1
  5Q GAIN WILD-TYPE     2                         7   145
D10V11, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1               154 
       TCGA-CH-5753        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-EJ-5542        TCGA-EJ-7123 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7791        TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5752        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-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5788        TCGA-CH-5789 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5496 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5532        TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7314 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        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-G9-6365 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075        TCGA-HC-7077 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7081 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7820        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     9   1
  6P GAIN WILD-TYPE 474   8
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               482 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                 8 
$`6P GAIN MUTATED`
TCGA-KC-A7FA TCGA-HI-7168 TCGA-KK-A59Z TCGA-V1-A8WV TCGA-XJ-A9DX TCGA-XK-AAJT 
       19.66       109.25        86.40        22.55        31.99        47.15 
TCGA-YL-A9WJ TCGA-ZG-A9L1 TCGA-ZG-A9LS TCGA-ZG-A9NI 
       60.99        42.81        16.96         4.34 

$`6P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP 
       31.43         3.48         7.00        32.61        40.67         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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        35.44 
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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
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        27.85        30.38 
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        15.55 
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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7169 
        9.53        25.48        18.84        19.30        27.75        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        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85        10.62        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       64.70       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        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        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
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-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 
       61.68        64.04        30.38        15.58        35.44         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
       48.03         9.04         2.99        31.96        37.25        40.04 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       30.58        41.39        36.95        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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        75.75        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        77.79        68.48         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        70.22        24.33        49.91        36.10         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-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 
       11.47        13.48 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             4.34              0.76 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           109.25            165.17 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           37.400            30.545 
[1] "4.3 - 109.2 (37.4)" "0.8 - 165.2 (30.5)"
[1] "hr=" "6.8"
D11V2, continuous
                   vv
clus                 T2  T3  T4
  6P GAIN MUTATED     1   9   0
  6P GAIN WILD-TYPE 186 279  10
D11V3, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T2               1               186
  T3               9               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"
D11V4, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5   5
  6P GAIN WILD-TYPE 338  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    5
  6P GAIN WILD-TYPE  338   72
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               5               338
  1               5                72
[1] 2 2
[1] FALSE
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     6   3
  6P GAIN WILD-TYPE 384  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    3
  6P GAIN WILD-TYPE  384   56
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                6               384
  YES               3                56
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    10   0
  6P GAIN WILD-TYPE 468  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     10    0
  6P GAIN WILD-TYPE  468   14
                                        clus
vv                                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 10               468
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED     4   6   0   0
  6P GAIN WILD-TYPE 309 138   5  15
D11V7, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               4               309
  R1               6               138
  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"
D11V8, continuous
D11V9, continuous
D11V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       0                         0     1
  6P GAIN WILD-TYPE     2                         7   145
D11V11, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1               154 
       TCGA-CH-5753        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-EJ-5542        TCGA-EJ-7123 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7791        TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5752        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-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5788        TCGA-CH-5789 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-7115        TCGA-EJ-7125 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"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-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820        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     6   0
  6Q GAIN WILD-TYPE 477   9
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               486 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 9 
$`6Q GAIN MUTATED`
TCGA-HI-7168 TCGA-KK-A59Z TCGA-XJ-A9DX TCGA-XK-AAJT TCGA-ZG-A9L1 TCGA-ZG-A9LS 
      109.25        86.40        31.99        47.15        42.81        16.96 

$`6Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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 
       28.83        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
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 
       35.44        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       27.12        13.87         5.85        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       35.44         6.64        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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 
       25.18        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 
      119.38        75.91       109.58       102.90        23.93        89.49 
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        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR 
       48.03        42.08        48.03         9.04         2.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       37.25        40.04        30.58        41.39        36.95        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         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        75.75        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        77.79        68.48 
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        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         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-A9LU TCGA-ZG-A9LY 
       20.28        19.17        12.43         3.78        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 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            16.96              0.76 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           109.25            165.17 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           44.980            30.445 
[1] "17.0 - 109.2 (45.0)" "0.8 - 165.2 (30.4)" 
[1] "hr="     "9200000"
D12V2, continuous
                   vv
clus                 T2  T3  T4
  6Q GAIN MUTATED     1   5   0
  6Q GAIN WILD-TYPE 186 283  10
D12V3, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T2               1               186
  T3               5               283
  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   3
  6Q GAIN WILD-TYPE 340  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    3
  6Q GAIN WILD-TYPE  340   74
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               3               340
  1               3                74
[1] 2 2
[1] FALSE
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3   2
  6Q GAIN WILD-TYPE 387  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    2
  6Q GAIN WILD-TYPE  387   57
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                3               387
  YES               2                57
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     6   0
  6Q GAIN WILD-TYPE 472  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6    0
  6Q GAIN WILD-TYPE  472   14
                                        clus
vv                                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  6               472
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED     2   4   0   0
  6Q GAIN WILD-TYPE 311 140   5  15
D12V7, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0               2               311
  R1               4               140
  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"
D12V8, continuous
D12V9, continuous
D12V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         0     1
  6Q GAIN WILD-TYPE     2                         7   145
D12V11, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1               154 
       TCGA-CH-5753        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-EJ-5542        TCGA-EJ-7123 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7791        TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5752        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-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5788        TCGA-CH-5789 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-7115        TCGA-EJ-7125 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"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-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820        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   101   0
  7P GAIN WILD-TYPE 382   9
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              101               391 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 9 
$`7P GAIN MUTATED`
TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-5542 TCGA-HC-A76W TCGA-J9-A8CN TCGA-KK-A7AP 
       15.98        33.01        49.74         7.00        40.67         6.44 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-4L-AA1F TCGA-CH-5751 
       32.45         2.73        41.00        41.49        11.51        35.01 
TCGA-CH-5754 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5788 TCGA-EJ-5494 TCGA-EJ-5495 
        2.04        24.03        13.02        26.99        48.56        57.86 
TCGA-EJ-5509 TCGA-EJ-5525 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7330 TCGA-EJ-7784 
       48.13        36.66        93.70        37.81         6.28        25.68 
TCGA-EJ-7786 TCGA-EJ-A46F TCGA-EJ-A65M TCGA-EJ-A7NH TCGA-EJ-A8FN TCGA-EJ-AB20 
       36.03        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        28.83        66.67        64.01        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        30.84        22.55 
TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AP TCGA-HC-A9TE 
       17.95        15.88         0.76         1.78         2.33        19.30 
TCGA-HI-7168 TCGA-J4-8198 TCGA-J9-A52E TCGA-J9-A8CL TCGA-KK-A59Z TCGA-KK-A6E8 
      109.25        20.19        10.62        13.32        86.40        58.19 
TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A8I4 TCGA-KK-A8IA TCGA-KK-A8IF TCGA-KK-A8IG 
       57.67        43.69        74.27        63.48        26.43        82.36 
TCGA-KK-A8IK TCGA-M7-A721 TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8WL TCGA-V1-A8WV 
       67.46        13.15        20.05        28.18        64.04        22.55 
TCGA-V1-A8WW TCGA-V1-A9O7 TCGA-V1-A9OX TCGA-V1-A9Z7 TCGA-V1-A9ZI TCGA-VN-A88P 
       35.44        82.16        37.28        28.73        53.92        41.42 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ 
      119.38        75.91        89.49        21.80        44.88        45.47 
TCGA-XJ-A83H TCGA-XK-AAIV TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       42.08        37.25         4.87        48.72        75.75        62.14 
TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       56.52        45.14       114.38        68.48         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A8QX TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9LB 
       53.36        70.22        14.53        11.67        42.81        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       12.43        22.75        17.98        11.47         4.34 

$`7P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-EJ-7123 TCGA-EJ-7312 
        1.02        12.00         1.02        32.02        84.56        36.13 
TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC 
       35.18        36.76        21.60        21.96        14.83        28.70 
TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ TCGA-J4-A83N 
       39.39        44.55        26.04        31.43         3.48        32.61 
TCGA-KC-A7FA TCGA-KK-A7B3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT 
       19.66        29.56        32.19        20.42        55.92        45.14 
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        45.30         3.68        28.37        44.84        41.82 
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-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 
        0.92        44.02        23.01         1.02        15.06         2.04 
TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
        9.99         2.99        29.00        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       45.40        47.90        64.60        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       74.93        68.35        61.87        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7317 
       41.85        60.10        88.34        83.57        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 
       33.83        27.09        30.35        27.68        24.39        35.28 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       38.37        25.87        38.70        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I 
       24.85        25.18        20.58        17.23        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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FO 
        8.22        14.20         6.48        15.65         4.21         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB 
        9.83         8.75         4.54         4.77        28.41        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       67.99        83.87        55.76        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6373 
       45.30        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        35.44        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 
       36.26        35.84        31.69        23.57        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        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-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F 
       27.85        30.38        22.32         1.58        15.55        22.36 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AS TCGA-HC-A6HX 
        2.01         2.20         1.61        17.42         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH 
        4.41         4.93         9.53        25.48        18.84        27.75 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       88.24        82.92        43.69        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       13.87         5.85        10.55        15.22        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-A6DY 
        8.88        11.57       113.10        83.34        64.70       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
      113.33        90.74        52.93        58.36        27.02        34.65 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       49.94        34.95        36.13       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8II 
       31.79        32.91        67.43        69.27        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       47.64        58.88        16.70        14.73        39.29        61.68 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA 
       30.38        15.58         6.64        63.52        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OY 
       38.93        79.00        62.89        12.20        15.65        35.08 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       27.19        17.75        49.87        45.47        44.75         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        25.18        15.81        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C 
       25.78        16.31       109.58       102.90        23.93        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS 
       60.92        66.97        58.32        42.94        14.76        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       12.36        37.05        48.03        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-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC 
       52.96        49.02        51.45        60.56        16.83        41.46 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP 
       28.77        53.06        45.86        46.29        32.45        77.79 
TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QY 
       60.99        24.33        49.91        36.10         3.09        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-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC 
       20.28         3.78        16.96        19.04        12.16        14.96 
TCGA-ZG-A9ND 
       13.48 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.76              0.89 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           119.38            165.17 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            33.01             30.38 
[1] "0.8 - 119.4 (33.0)" "0.9 - 165.2 (30.4)"
[1] "hr="     "2.7e+08"
D13V2, continuous
                   vv
clus                 T2  T3  T4
  7P GAIN MUTATED    29  71   1
  7P GAIN WILD-TYPE 158 217   9
D13V3, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T2              29               158
  T3              71               217
  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  19
  7P GAIN WILD-TYPE 274  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     69   19
  7P GAIN WILD-TYPE  274   58
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              69               274
  1              19                58
[1] 2 2
[1] FALSE
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    75  14
  7P GAIN WILD-TYPE 315  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     75   14
  7P GAIN WILD-TYPE  315   45
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               75               315
  YES              14                45
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    99   2
  7P GAIN WILD-TYPE 379  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     99    2
  7P GAIN WILD-TYPE  379   12
                                        clus
vv                                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 99               379
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               2                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED    49  44   1   4
  7P GAIN WILD-TYPE 264 100   4  11
D13V7, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              49               264
  R1              44               100
  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"
D13V8, continuous
D13V9, continuous
D13V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       0                         0    26
  7P GAIN WILD-TYPE     2                         7   120
D13V11, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  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    94   0
  7Q GAIN WILD-TYPE 389   9
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               94               398 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 9 
$`7Q GAIN MUTATED`
TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-5542 TCGA-HC-A76W TCGA-J9-A8CN TCGA-KK-A7AP 
       15.98        33.01        49.74         7.00        40.67         6.44 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5768 
       32.45         2.73        41.00        11.51        35.01        24.03 
TCGA-CH-5771 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5509 TCGA-EJ-5525 TCGA-EJ-7125 
       13.02        48.56        57.86        48.13        36.66        93.70 
TCGA-EJ-7314 TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-A46F TCGA-EJ-A65M TCGA-EJ-A7NH 
       37.81         6.28        25.68        25.74         7.56        15.58 
TCGA-EJ-A8FN TCGA-EJ-AB20 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6366 
       10.82         4.31        15.42        28.83        66.67        64.01 
TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7523 
       40.31        31.50        56.75        64.18        50.73        28.18 
TCGA-HC-7742 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 
       30.84        22.55        17.95        15.88         0.76         1.78 
TCGA-HC-A6AP TCGA-HC-A9TE TCGA-HI-7168 TCGA-J4-8198 TCGA-J9-A52E TCGA-J9-A8CL 
        2.33        19.30       109.25        20.19        10.62        13.32 
TCGA-KK-A59Z TCGA-KK-A6E8 TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A8IA TCGA-KK-A8IF 
       86.40        58.19        57.67        43.69        63.48        26.43 
TCGA-KK-A8IG TCGA-KK-A8IK TCGA-M7-A721 TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8WL 
       82.36        67.46        13.15        20.05        28.18        64.04 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A9O7 TCGA-V1-A9OX TCGA-V1-A9Z7 TCGA-V1-A9ZI 
       22.55        35.44        82.16        37.28        28.73        53.92 
TCGA-VN-A88P TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-AA1N 
       41.42       119.38        75.91        89.49        21.80        44.88 
TCGA-X4-A8KQ TCGA-XJ-A83H TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       45.47        42.08         4.87        48.72        75.75        62.14 
TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       56.52        45.14       114.38        68.48         8.98        14.04 
TCGA-YL-A9WK TCGA-ZG-A8QX TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       70.22        14.53        11.67        42.81        19.17        12.43 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       22.75        17.98        11.47         4.34 

$`7Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-EJ-7123 TCGA-EJ-7312 
        1.02        12.00         1.02        32.02        84.56        36.13 
TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC 
       35.18        36.76        21.60        21.96        14.83        28.70 
TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ TCGA-J4-A83N 
       39.39        44.55        26.04        31.43         3.48        32.61 
TCGA-KC-A7FA TCGA-KK-A7B3 TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
       19.66        29.56        41.49        32.19        20.42        55.92 
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       45.14        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 
       41.82        20.22         2.99         6.97        22.06         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       12.99        13.97         1.97        24.03         1.02        13.02 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
       15.06         2.04        26.99         9.99         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        56.55        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        46.92        30.31        45.40        47.90        64.60 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       62.04        48.53        56.98        60.13        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        69.63        64.50        74.93        68.35        61.87 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       83.57        33.14        25.35        33.83        27.09        30.35 
TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
       27.68        24.39        35.28        38.37        25.87        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       20.58        17.23        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       13.71        18.41        21.90        11.61         8.22        14.20 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        6.48        15.65         4.21         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.54         4.77        28.41        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 
       20.25        41.62        87.35        81.04        67.99        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 
       40.18        39.95        38.01        26.66        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       30.97        35.44        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       31.69        23.57        17.46        23.70        24.59        23.80 
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        27.85        30.38 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL 
       22.32         1.58        15.55        22.36         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
        1.61        17.42         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        27.75        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       43.69        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       10.55        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-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        83.34        64.70       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B1 
       52.93        58.36        27.02        34.65        49.94        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       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        62.96        16.21        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-TK-A8OK TCGA-TP-A8TT TCGA-V1-A8MF 
      122.17        86.14        18.12         0.89        17.29        47.64 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN 
       58.88        16.70        14.73        39.29        61.68        30.38 
TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       15.58         6.64        63.52        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OY TCGA-V1-A9Z8 
       79.00        62.89        12.20        15.65        35.08        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87        45.47        44.75         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        25.18        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       102.90        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        58.32        42.94        14.76        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       37.05        48.03        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC 
       52.96        49.02        51.45        60.56        16.83        41.46 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP 
       28.77        53.06        45.86        46.29        32.45        77.79 
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        36.10         3.09 
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-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       22.59        20.28         3.78        16.96        19.04        12.16 
TCGA-ZG-A9MC TCGA-ZG-A9ND 
       14.96        13.48 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.76              0.89 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           119.38            165.17 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           31.975            30.445 
[1] "0.8 - 119.4 (32.0)" "0.9 - 165.2 (30.4)"
[1] "hr="     "2.6e+08"
D14V2, continuous
                   vv
clus                 T2  T3  T4
  7Q GAIN MUTATED    28  65   1
  7Q GAIN WILD-TYPE 159 223   9
D14V3, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T2              28               159
  T3              65               223
  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  14
  7Q GAIN WILD-TYPE 276  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     67   14
  7Q GAIN WILD-TYPE  276   63
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              67               276
  1              14                63
[1] 2 2
[1] FALSE
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    70  13
  7Q GAIN WILD-TYPE 320  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     70   13
  7Q GAIN WILD-TYPE  320   46
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               70               320
  YES              13                46
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    92   2
  7Q GAIN WILD-TYPE 386  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     92    2
  7Q GAIN WILD-TYPE  386   12
                                        clus
vv                                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 92               386
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               2                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED    44  42   1   4
  7Q GAIN WILD-TYPE 269 102   4  11
D14V7, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              44               269
  R1              42               102
  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"
D14V8, continuous
D14V9, continuous
D14V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       0                         0    23
  7Q GAIN WILD-TYPE     2                         7   123
D14V11, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  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    67   1
  8P GAIN WILD-TYPE 416   8
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               68               424 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                 8 
$`8P GAIN MUTATED`
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-A65J TCGA-KK-A8IB TCGA-4L-AA1F TCGA-CH-5751 
       84.56        36.13        14.83         2.73        11.51        35.01 
TCGA-CH-5761 TCGA-EJ-5504 TCGA-EJ-5509 TCGA-EJ-5514 TCGA-EJ-5521 TCGA-EJ-5525 
        0.92        46.92        48.13        60.13        74.93        36.66 
TCGA-EJ-5526 TCGA-EJ-7125 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-A65M TCGA-EJ-A7NH 
       62.76        93.70        25.68        36.33         7.56        15.58 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 TCGA-HC-7078 
       15.42        28.83        50.73        38.96        30.97        65.26 
TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A6AO TCGA-HC-A8CY 
       30.84        23.70        15.88         0.76        17.42         9.53 
TCGA-J9-A52B TCGA-J9-A8CM TCGA-KK-A59V TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E8 
       13.87        15.22       113.10        86.40       141.21        58.19 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IK TCGA-M7-A724 TCGA-QU-A6IL TCGA-V1-A8MF 
       65.82        31.79        67.46        29.23         3.19        47.64 
TCGA-V1-A8MM TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9ZI 
       39.29        22.55        63.52        28.73        27.19        53.92 
TCGA-VN-A88M TCGA-VN-A943 TCGA-VP-A87H TCGA-VP-AA1N TCGA-XK-AAJT TCGA-YL-A8HM 
        6.21        16.31        21.80        44.88        47.15        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SK TCGA-YL-A8SQ TCGA-YL-A9WJ 
       75.75        62.14        60.56        46.29        68.48        60.99 
TCGA-YL-A9WK TCGA-ZG-A9L1 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       70.22        42.81        29.85        22.59        19.17        12.43 
TCGA-ZG-A9LU TCGA-ZG-A9LZ 
       19.04        22.75 

$`8P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A6RC 
       49.74        35.18        36.76        21.60        21.96        28.70 
TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W 
       39.39        44.55        26.04        31.43         3.48         7.00 
TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 
       32.61        40.67        19.66         6.44        29.56        32.45 
TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT 
       41.00        41.49        32.19        20.42        55.92        45.14 
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        45.30         3.68        28.37        44.84        41.82 
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-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        2.04        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       44.88        38.50        45.73        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       64.60        62.04        48.53        56.98        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5527 
       62.10        69.63        64.50        68.35        61.87        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7218 TCGA-EJ-7314 
       60.23        41.85        60.10        88.34        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       36.03        28.24        45.90         3.75        42.94        32.32 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       77.16        76.41        38.10        24.85        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       13.71        18.41        21.90        11.61         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-A5OB 
        8.75         4.54         4.31         4.77        28.41        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        35.44        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        69.53        38.93 
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        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       31.69        23.57        17.46        24.59        23.80        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        27.85        30.38        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 
       17.95        22.32         1.58        15.55        22.36         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.01         2.20         1.61         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.41         4.93        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.55        27.12         5.85        10.62        10.55        13.32 
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-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
       21.86         8.65         8.88        11.57        83.34        64.70 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
      113.33        90.74        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-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
      101.79        21.96        32.91        63.48        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 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       25.08        18.84         5.69       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12         0.89        17.29        20.05        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       16.70        14.73        61.68        64.04        30.38        15.58 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       35.44         6.64        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87        45.47        44.75         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
       24.53        25.18        15.81        41.42        44.91        25.78 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      119.38        75.91       109.58       102.90        23.93        89.49 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       55.56        60.92        66.97        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XQ-A8TA 
       40.04        30.58        41.39        36.95        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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        77.79         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        36.10         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-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.76              0.89 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           141.21            165.17 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           35.570            30.365 
[1] "0.8 - 141.2 (35.6)" "0.9 - 165.2 (30.4)"
[1] "hr=" "1.5"
D15V2, continuous
                   vv
clus                 T2  T3  T4
  8P GAIN MUTATED    16  49   3
  8P GAIN WILD-TYPE 171 239   7
D15V3, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T2              16               171
  T3              49               239
  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    53  13
  8P GAIN WILD-TYPE 290  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     53   13
  8P GAIN WILD-TYPE  290   64
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              53               290
  1              13                64
[1] 2 2
[1] FALSE
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    53  11
  8P GAIN WILD-TYPE 337  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     53   11
  8P GAIN WILD-TYPE  337   48
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               53               337
  YES              11                48
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    68   0
  8P GAIN WILD-TYPE 410  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     68    0
  8P GAIN WILD-TYPE  410   14
                                        clus
vv                                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 68               410
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    33  31   1   1
  8P GAIN WILD-TYPE 280 113   4  14
D15V7, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              33               280
  R1              31               113
  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"
D15V8, continuous
D15V9, continuous
D15V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         1    16
  8P GAIN WILD-TYPE     2                         6   130
D15V11, 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   124   2
  8Q GAIN WILD-TYPE 359   7
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              126               366 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 7 
$`8Q GAIN MUTATED`
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-A46G TCGA-EJ-A65J TCGA-KK-A8IB TCGA-2A-A8VV 
       84.56        36.13        21.96        14.83         2.73        22.06 
TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5771 
       45.30         3.68        11.51        35.01         0.92        13.02 
TCGA-EJ-5504 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5521 
       46.92        48.13        48.53        60.13        62.10        74.93 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5532 TCGA-EJ-7125 TCGA-EJ-7781 TCGA-EJ-7784 
       36.66        62.76        60.10        93.70        35.28        25.68 
TCGA-EJ-7789 TCGA-EJ-8469 TCGA-EJ-A46F TCGA-EJ-A65M TCGA-EJ-A7NH TCGA-EJ-AB27 
       36.33        76.41        25.74         7.56        15.58         4.77 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6494 
       15.42        28.83        64.01        26.66        31.50        58.22 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S7 TCGA-HC-7078 
       50.73        52.93        38.96        30.97        23.93        65.26 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-8216 TCGA-HC-8265 
       28.60        40.08        30.84        23.70        22.42        15.88 
TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A8CY 
       15.55         0.76         2.01         2.20        17.42         9.53 
TCGA-HC-A9TE TCGA-J4-A67M TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       19.30        30.94        13.87        10.62        13.32        15.22 
TCGA-KC-A4BV TCGA-KK-A59V TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E8 TCGA-KK-A7AU 
       43.66       113.10        86.40       141.21        58.19        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       27.02        34.65        74.27        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IG TCGA-KK-A8IK TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       63.48        82.36        67.46        29.23        18.84         3.19 
TCGA-QU-A6IO TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MM TCGA-V1-A8WV TCGA-V1-A9O5 
      122.17        47.64        28.18        39.29        22.55        63.52 
TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       82.16        20.91        79.00        62.89        28.73        27.19 
TCGA-V1-A9ZI TCGA-VN-A88M TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A87H 
       53.92         6.21        41.42        16.31        75.91        21.80 
TCGA-VP-AA1N TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XK-AAIV TCGA-XK-AAJT TCGA-XQ-A8TA 
       44.88        48.03        42.08        37.25        47.15         4.80 
TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SK 
        4.87        48.72        75.75        62.14        60.56        46.29 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WY 
       68.48         8.98        14.04        60.99        70.22        36.10 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       11.67        42.81        29.85        22.59        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       12.43        19.04        12.16        22.75        11.47         4.34 

$`8Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A6RC TCGA-G9-6364 
       49.74        35.18        36.76        21.60        28.70        39.39 
TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N 
       44.55        26.04        31.43         3.48         7.00        32.61 
TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-QU-A6IM 
       40.67        19.66         6.44        29.56        32.45        41.00 
TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8W3 
       41.49        32.19        20.42        55.92        45.14        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       44.84        41.82        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-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       13.02        31.00         2.04        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       15.06        24.03         2.04        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 
       46.52        44.88        38.50        45.73        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       47.90        64.60        62.04        56.98        60.23        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5527 TCGA-EJ-5530 
       69.63        64.50        68.35        61.87        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-7115 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       41.85        88.34        83.57        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       33.83        27.09        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-7792 
       38.37        25.87        38.70        36.03        28.24        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 
        3.75        42.94        32.32        77.16        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       25.18        20.58        17.23        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A7NF 
       12.92        13.71        18.41        21.90        11.61         8.22 
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-FC-7708 TCGA-FC-A5OB 
        9.83         8.75         4.54         4.31        28.41        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       47.44        45.30        44.81        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 
       40.31        37.97        58.45        25.15        27.29        56.75 
TCGA-G9-6498 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       64.18        27.91        35.44        28.18        32.68        26.01 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        69.53        38.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7230 
       36.36        37.35        14.47        28.54        40.14        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       17.46        24.59        23.80        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 
       27.85        30.38        22.55        17.95        22.32         1.58 
TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
       22.36         1.78         1.61         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH TCGA-HI-7168 
        4.41         4.93        25.48        18.84        27.75       109.25 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       25.32        30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
        5.85        10.55        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-A59X 
       44.35        21.86         8.65         8.88        11.57        83.34 
TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       64.70        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AY TCGA-KK-A7AZ 
       68.15       113.33        90.74        52.93        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8IC 
       43.69        34.95        36.13       101.79        21.96        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL 
       69.27        26.43        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 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-MG-AAMC TCGA-QU-A6IN TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
       25.08         5.69       140.19        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU 
       17.29        20.05        58.88        16.70        14.73        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O9 
       64.04        30.38        15.58        35.44         6.64        94.36 
TCGA-V1-A9OF TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z9 
       38.93        12.20        15.65        37.28        35.08        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87        45.47        44.75         8.84        25.51        24.53 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A876 
       25.18        15.81        44.91        25.78       119.38       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       58.32        42.94        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       37.05        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XQ-A8TB 
       40.04        30.58        41.39        36.95        51.81        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA 
       32.61        17.29        52.96        49.02        51.45        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-A9WI TCGA-YL-A9WL TCGA-YL-A9WX 
       32.45       114.38        77.79        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              0.89 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           141.21            165.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           31.645            30.365 
[1] "0.8 - 141.2 (31.6)" "0.9 - 165.2 (30.4)"
[1] "hr=" "1.4"
D16V2, continuous
                   vv
clus                 T2  T3  T4
  8Q GAIN MUTATED    30  91   4
  8Q GAIN WILD-TYPE 157 197   6
D16V3, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T2              30               157
  T3              91               197
  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"
D16V4, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    90  26
  8Q GAIN WILD-TYPE 253  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     90   26
  8Q GAIN WILD-TYPE  253   51
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              90               253
  1              26                51
[1] 2 2
[1] FALSE
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    95  19
  8Q GAIN WILD-TYPE 295  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     95   19
  8Q GAIN WILD-TYPE  295   40
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               95               295
  YES              19                40
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   124   2
  8Q GAIN WILD-TYPE 354  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    124    2
  8Q GAIN WILD-TYPE  354   12
                                        clus
vv                                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                124               354
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               2                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED    62  53   1   5
  8Q GAIN WILD-TYPE 251  91   4  10
D16V7, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              62               251
  R1              53                91
  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"
D16V8, continuous
D16V9, continuous
D16V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       0                         2    26
  8Q GAIN WILD-TYPE     2                         5   120
D16V11, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               2                 5
  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(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    33   1
  9P GAIN WILD-TYPE 450   8
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               34               458 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                 8 
$`9P GAIN MUTATED`
TCGA-CH-5791 TCGA-HC-7821 TCGA-CH-5771 TCGA-EJ-5495 TCGA-EJ-5514 TCGA-EJ-5526 
       33.01        31.43        13.02        57.86        60.13        62.76 
TCGA-EJ-7789 TCGA-EJ-A65F TCGA-FC-A4JI TCGA-HC-8266 TCGA-HC-A8CY TCGA-HC-A9TE 
       36.33        18.41        28.83        15.55         9.53        19.30 
TCGA-J4-AATZ TCGA-KK-A8I4 TCGA-V1-A8MJ TCGA-V1-A8WV TCGA-V1-A9OL TCGA-VP-A872 
       13.55        74.27        58.88        22.55        62.89       119.38 
TCGA-VP-A875 TCGA-VP-A87H TCGA-XK-AAIV TCGA-XQ-A8TA TCGA-YL-A8HO TCGA-YL-A8SC 
       75.91        21.80        37.25         4.80        75.75        41.46 
TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WK TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L5 
       32.45        68.48        70.22        11.67        42.81        29.85 
TCGA-ZG-A9LB TCGA-ZG-A9LS TCGA-ZG-A9M4 TCGA-ZG-A9NI 
       19.17        16.96        17.98         4.34 

$`9P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-EJ-5542 
        1.02        12.00         1.02        15.98        32.02        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-A6AQ 
       14.83        28.70        39.39        44.55        26.04         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 
        7.00        32.61        40.67        19.66         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 
       26.99         9.99         2.99        29.00        48.56        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       46.92        30.31        45.40        47.90        64.60        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       62.04        48.53        56.98        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        64.50        74.93        68.35        61.87        36.66 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7792 
       25.87        25.68        38.70        36.03        28.24        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65M 
       21.96        23.34        12.92        13.71        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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 
       25.94        20.25        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        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH 
        1.25         4.41         4.93        25.48        18.84        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       27.12        13.87         5.85        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 
       49.94        43.69        34.95        36.13       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       20.05        47.64        28.18        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 
       61.68        64.04        30.38        15.58        35.44         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         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        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       44.91        25.78        16.31       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       89.49        55.56        60.92        66.97        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        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-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
       51.81        25.32        32.61        17.29         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-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        77.79         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        36.10         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-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC 
       12.43         3.78        19.04        12.16        22.75        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       11.47        13.48 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             4.34              0.76 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           119.38            165.17 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           31.940            30.545 
[1] "4.3 - 119.4 (31.9)" "0.8 - 165.2 (30.5)"
[1] "hr=" "1.3"
D17V2, continuous
                   vv
clus                 T2  T3  T4
  9P GAIN MUTATED     2  30   1
  9P GAIN WILD-TYPE 185 258   9
D17V3, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T2               2               185
  T3              30               258
  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    18  14
  9P GAIN WILD-TYPE 325  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     18   14
  9P GAIN WILD-TYPE  325   63
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              18               325
  1              14                63
[1] 2 2
[1] FALSE
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    26   7
  9P GAIN WILD-TYPE 364  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     26    7
  9P GAIN WILD-TYPE  364   52
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               26               364
  YES               7                52
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    32   2
  9P GAIN WILD-TYPE 446  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     32    2
  9P GAIN WILD-TYPE  446   12
                                        clus
vv                                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 32               446
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               2                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    14  17   1   0
  9P GAIN WILD-TYPE 299 127   4  15
D17V7, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              14               299
  R1              17               127
  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"
D17V8, continuous
D17V9, continuous
D17V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         1     6
  9P GAIN WILD-TYPE     2                         6   140
D17V11, 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   1
  9Q GAIN WILD-TYPE 436   8
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               48               444 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                 8 
$`9Q GAIN MUTATED`
TCGA-CH-5791 TCGA-EJ-A46G TCGA-HC-7821 TCGA-CH-5751 TCGA-CH-5771 TCGA-EJ-5495 
       33.01        21.96        31.43        35.01        13.02        57.86 
TCGA-EJ-5496 TCGA-EJ-5526 TCGA-EJ-7789 TCGA-EJ-8472 TCGA-EJ-A65F TCGA-FC-A4JI 
       19.56        62.76        36.33        24.85        18.41        28.83 
TCGA-G9-6356 TCGA-G9-6373 TCGA-HC-8216 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A8CY 
       47.15        26.66        22.42        15.55         0.76         9.53 
TCGA-HC-A9TE TCGA-J4-AATZ TCGA-KK-A59Z TCGA-KK-A7AU TCGA-KK-A8I4 TCGA-V1-A8MJ 
       19.30        13.55        86.40        58.36        74.27        58.88 
TCGA-V1-A8WV TCGA-V1-A9OL TCGA-VN-A88K TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87D 
       22.55        62.89        25.51       119.38        75.91        60.92 
TCGA-VP-A87H TCGA-X4-A8KQ TCGA-XK-AAIV TCGA-XQ-A8TA TCGA-YL-A8HO TCGA-YL-A8SC 
       21.80        45.47        37.25         4.80        75.75        41.46 
TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WK TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L5 
       32.45        68.48        70.22        11.67        42.81        29.85 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9M4 TCGA-ZG-A9NI 
       20.28        19.17         3.78        16.96        17.98         4.34 

$`9Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-EJ-5542 
        1.02        12.00         1.02        15.98        32.02        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A65J 
       84.56        36.13        35.18        36.76        21.60        14.83 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-A6AQ TCGA-HC-A76W 
       28.70        39.39        44.55        26.04         3.48         7.00 
TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 
       32.61        40.67        19.66         6.44        29.56        32.45 
TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
        2.73        41.00        41.49        32.19        20.42        55.92 
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       45.14        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       41.82        20.22        11.51         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-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 
       13.02        31.00         2.04         0.92        44.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5789 
        1.02        15.06        24.03         2.04        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
        2.99        29.00        48.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 
       74.93        68.35        61.87        36.66        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       38.70        36.03        28.24        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46D 
       32.32        77.16        76.41        38.10        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       13.71        21.90         7.56        11.61         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        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
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        64.01        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-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87        27.85        30.38        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 
       22.32         1.58        15.88        22.36         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH TCGA-HI-7168 
        4.41         4.93        25.48        18.84        27.75       109.25 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AAU2 
       22.88        10.78        23.67        17.85        18.18        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85        10.62        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       64.70       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        58.19        52.93 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       36.13       101.79        21.96        65.82        31.79        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-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        67.46        20.65        62.96        16.21 
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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        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        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        35.44         6.64        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       20.91        38.93        79.00        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       45.47        44.75         8.84        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 
       15.81        41.42        44.91        25.78        16.31       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87J 
      102.90        23.93        89.49        55.56        66.97        58.32 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        44.88        14.76        32.19        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        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-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
       51.81        25.32        32.61        17.29         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-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        77.79         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        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LM 
       10.13         4.27        37.94        36.43        22.59        12.43 
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 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.76              0.89 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           119.38            165.17 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            29.34             30.76 
[1] "0.8 - 119.4 (29.3)" "0.9 - 165.2 (30.8)"
[1] "hr=" "1"  
D18V2, continuous
                   vv
clus                 T2  T3  T4
  9Q GAIN MUTATED     3  42   2
  9Q GAIN WILD-TYPE 184 246   8
D18V3, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T2               3               184
  T3              42               246
  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 318  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     25   20
  9Q GAIN WILD-TYPE  318   57
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              25               318
  1              20                57
[1] 2 2
[1] FALSE
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    37   9
  9Q GAIN WILD-TYPE 353  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     37    9
  9Q GAIN WILD-TYPE  353   50
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               37               353
  YES               9                50
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    45   3
  9Q GAIN WILD-TYPE 433  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     45    3
  9Q GAIN WILD-TYPE  433   11
                                        clus
vv                                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 45               433
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               3                11
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    21  23   1   1
  9Q GAIN WILD-TYPE 292 121   4  14
D18V7, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              21               292
  R1              23               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"
D18V8, continuous
D18V9, continuous
D18V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         1     9
  9Q GAIN WILD-TYPE     2                         6   137
D18V11, 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    15   0
  10P GAIN WILD-TYPE 468   9
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                15                477 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  9 
$`10P GAIN MUTATED`
TCGA-EJ-5514 TCGA-EJ-8469 TCGA-G9-6499 TCGA-HC-7078 TCGA-HC-7231 TCGA-HC-7742 
       60.13        76.41        50.73        65.26        30.87        30.84 
TCGA-HC-A9TE TCGA-KK-A7AV TCGA-V1-A8WV TCGA-VP-A872 TCGA-YL-A9WH TCGA-YL-A9WY 
       19.30        27.02        22.55       119.38        14.04        36.10 
TCGA-ZG-A9LM TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       12.43        11.47         4.34 

$`10P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       56.98        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 
        3.75        42.94        32.32        77.16        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       69.53        38.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7736 
       40.14        28.60        40.08        32.91        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       35.84        31.69        23.57        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH TCGA-HI-7168 
        4.93         9.53        25.48        18.84        27.75       109.25 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       27.12        13.87         5.85        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       58.19        52.93        58.36        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW 
       39.29        61.68        64.04        30.38        15.58        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         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        75.75        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        77.79        68.48 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
        8.98        53.36        60.99        70.22        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-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        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-A9LZ 
       19.17         3.78        16.96        19.04        12.16        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND 
       17.98        14.96        13.48 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              4.34               0.76 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            119.38             165.17 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             30.84              30.58 
[1] "4.3 - 119.4 (30.8)" "0.8 - 165.2 (30.6)"
[1] "hr="     "2.9e+07"
D19V2, continuous
                    vv
clus                  T2  T3  T4
  10P GAIN MUTATED     3  12   0
  10P GAIN WILD-TYPE 184 276  10
D19V3, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T2                3                184
  T3               12                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"
D19V4, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     9   5
  10P GAIN WILD-TYPE 334  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9    5
  10P GAIN WILD-TYPE  334   72
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                9                334
  1                5                 72
[1] 2 2
[1] FALSE
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    14   1
  10P GAIN WILD-TYPE 376  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     14    1
  10P GAIN WILD-TYPE  376   58
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                14                376
  YES                1                 58
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    14   1
  10P GAIN WILD-TYPE 464  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     14    1
  10P GAIN WILD-TYPE  464   13
                                        clus
vv                                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  14                464
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED     8   5   0   2
  10P GAIN WILD-TYPE 305 139   5  13
D19V7, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                8                305
  R1                5                139
  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"
D19V8, continuous
D19V9, continuous
D19V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0     5
  10P GAIN WILD-TYPE     2                         7   141
D19V11, 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    14   0
  10Q GAIN WILD-TYPE 469   9
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                478 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                  9 
$`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        60.13        76.41        65.26        30.87 
TCGA-HC-7742 TCGA-HC-A9TE TCGA-KK-A7AV TCGA-V1-A8WV TCGA-VP-A872 TCGA-YL-A8SQ 
       30.84        19.30        27.02        22.55       119.38        68.48 
TCGA-YL-A9WY TCGA-ZG-A9N3 
       36.10        11.47 

$`10Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        2.04        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        2.04        13.02         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 
       64.60        48.13        62.04        48.53        56.98        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        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        35.28        38.37        25.87        25.68        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       32.32        77.16        38.10        24.85        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         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        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        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        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        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        35.44        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       28.60        40.08        32.91        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       31.69        23.57        17.46        23.70        24.59        23.80 
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        27.85        30.38 
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        15.55 
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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
        9.53        25.48        18.84        27.75       109.25        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        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85        10.62        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       52.93        58.36        34.65        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
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-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 
       61.68        64.04        30.38        15.58        35.44         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78        16.31        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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        75.75        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        77.79         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        70.22        24.33        49.91         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       14.53        13.28        10.13         4.27        11.67        42.81 
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 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.92               0.76 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            119.38             165.17 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            30.855             30.545 
[1] "0.9 - 119.4 (30.9)" "0.8 - 165.2 (30.5)"
[1] "hr="     "2.9e+07"
D20V2, continuous
                    vv
clus                  T2  T3  T4
  10Q GAIN MUTATED     3  11   0
  10Q GAIN WILD-TYPE 184 277  10
D20V3, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T2                3                184
  T3               11                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"
D20V4, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     9   4
  10Q GAIN WILD-TYPE 334  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      9    4
  10Q GAIN WILD-TYPE  334   73
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                9                334
  1                4                 73
[1] 2 2
[1] FALSE
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    13   0
  10Q GAIN WILD-TYPE 377  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     13    0
  10Q GAIN WILD-TYPE  377   59
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                13                377
  YES                0                 59
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    13   1
  10Q GAIN WILD-TYPE 465  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     13    1
  10Q GAIN WILD-TYPE  465   13
                                        clus
vv                                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  13                465
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED     8   4   0   2
  10Q GAIN WILD-TYPE 305 140   5  13
D20V7, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                8                305
  R1                4                140
  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"
D20V8, continuous
D20V9, continuous
D20V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     6
  10Q GAIN WILD-TYPE     2                         7   140
D20V11, 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    27   0
  11P GAIN WILD-TYPE 456   9
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                465 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  9 
$`11P GAIN MUTATED`
TCGA-HC-A76W TCGA-KC-A7FA TCGA-4L-AA1F TCGA-CH-5751 TCGA-EJ-5495 TCGA-EJ-5511 
        7.00        19.66        11.51        35.01        57.86        48.53 
TCGA-EJ-7784 TCGA-G9-7523 TCGA-HC-8216 TCGA-HC-A9TE TCGA-HI-7168 TCGA-J4-AATZ 
       25.68        28.18        22.42        19.30       109.25        13.55 
TCGA-KK-A6E8 TCGA-KK-A8I4 TCGA-V1-A8WV TCGA-X4-A8KS TCGA-YL-A8HM TCGA-YL-A8SQ 
       58.19        74.27        22.55        32.19        48.72        68.48 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L5 TCGA-ZG-A9LB 
       14.04        53.36        11.67        42.81        29.85        19.17 
TCGA-ZG-A9LS TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       16.96        22.75        17.98 

$`11P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP TCGA-KK-A7B3 
       31.43         3.48        32.61        40.67         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       44.84        41.82        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-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 
       13.02        31.00         2.04         0.92        44.02        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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 
        9.99         2.99        29.00        48.56        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       56.55        46.52        44.88        38.50        45.73        46.92 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.87        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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        35.44 
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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87        27.85        30.38        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        15.55        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-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-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        27.75        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK 
       18.18        27.12        13.87         5.85        10.62        10.55 
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        83.34        64.70        86.40       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       90.74        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 
       49.94        43.69        34.95        36.13       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW 
       39.29        61.68        64.04        30.38        15.58        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58       102.90        23.93        89.49        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        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       14.76        45.47        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         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        75.75        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-A9WJ 
       46.29        32.45       114.38        77.79         8.98        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       70.22        24.33        49.91        36.10         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-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC 
       20.28        12.43         3.78        19.04        12.16        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              7.00               0.76 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            109.25             165.17 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             25.68              30.84 
[1] "7.0 - 109.2 (25.7)" "0.8 - 165.2 (30.8)"
[1] "hr="     "2.6e+07"
D21V2, continuous
                    vv
clus                  T2  T3  T4
  11P GAIN MUTATED     3  22   2
  11P GAIN WILD-TYPE 184 266   8
D21V3, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T2                3                184
  T3               22                266
  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    15  11
  11P GAIN WILD-TYPE 328  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     15   11
  11P GAIN WILD-TYPE  328   66
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               15                328
  1               11                 66
[1] 2 2
[1] FALSE
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    20   6
  11P GAIN WILD-TYPE 370  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     20    6
  11P GAIN WILD-TYPE  370   53
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                20                370
  YES                6                 53
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    27   0
  11P GAIN WILD-TYPE 451  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     27    0
  11P GAIN WILD-TYPE  451   14
                                        clus
vv                                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  27                451
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    10  15   0   2
  11P GAIN WILD-TYPE 303 129   5  13
D21V7, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               10                303
  R1               15                129
  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"
D21V8, continuous
D21V9, continuous
D21V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         1     4
  11P GAIN WILD-TYPE     2                         6   142
D21V11, 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    30   0
  11Q GAIN WILD-TYPE 453   9
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                30                462 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  9 
$`11Q GAIN MUTATED`
TCGA-HC-A76W TCGA-KC-A7FA TCGA-4L-AA1F TCGA-CH-5751 TCGA-EJ-5495 TCGA-EJ-5511 
        7.00        19.66        11.51        35.01        57.86        48.53 
TCGA-EJ-7784 TCGA-EJ-8472 TCGA-G9-7523 TCGA-HC-8216 TCGA-HC-A9TE TCGA-HI-7168 
       25.68        24.85        28.18        22.42        19.30       109.25 
TCGA-KK-A6E8 TCGA-KK-A8I4 TCGA-KK-A8IK TCGA-V1-A8WV TCGA-X4-A8KS TCGA-YL-A8HM 
       58.19        74.27        67.46        22.55        32.19        48.72 
TCGA-YL-A8SB TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       56.52        68.48        14.04        53.36        11.67        42.81 
TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LS TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       29.85        19.17        16.96        22.75        17.98        11.47 

$`11Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP TCGA-KK-A7B3 
       31.43         3.48        32.61        40.67         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       44.84        41.82        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-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 
       13.02        31.00         2.04         0.92        44.02        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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 
        9.99         2.99        29.00        48.56        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       56.55        46.52        44.88        38.50        45.73        46.92 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.87        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 
       30.51        30.84        17.85        24.56        19.36        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       27.75        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK 
       13.55        27.12        13.87         5.85        10.62        10.55 
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        83.34        64.70        86.40       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       90.74        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 
       49.94        43.69        34.95        36.13       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 
       61.68        64.04        30.38        15.58        35.44         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        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        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       45.47        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC 
       51.45        75.75        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-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
      114.38        77.79         8.98        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM 
        4.27        37.94        36.43        22.59        20.28        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
        3.78        19.04        12.16        14.96        13.48         4.34 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              7.00               0.76 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            109.25             165.17 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            26.930             30.825 
[1] "7.0 - 109.2 (26.9)" "0.8 - 165.2 (30.8)"
[1] "hr="     "2.7e+07"
D22V2, continuous
                    vv
clus                  T2  T3  T4
  11Q GAIN MUTATED     4  24   2
  11Q GAIN WILD-TYPE 183 264   8
D22V3, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T2                4                183
  T3               24                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"
D22V4, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    17  12
  11Q GAIN WILD-TYPE 326  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     17   12
  11Q GAIN WILD-TYPE  326   65
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               17                326
  1               12                 65
[1] 2 2
[1] FALSE
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    23   6
  11Q GAIN WILD-TYPE 367  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     23    6
  11Q GAIN WILD-TYPE  367   53
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                23                367
  YES                6                 53
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    30   0
  11Q GAIN WILD-TYPE 448  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     30    0
  11Q GAIN WILD-TYPE  448   14
                                        clus
vv                                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  30                448
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    12  16   0   2
  11Q GAIN WILD-TYPE 301 128   5  13
D22V7, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               12                301
  R1               16                128
  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"
D22V8, continuous
D22V9, continuous
D22V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         1     4
  11Q GAIN WILD-TYPE     2                         6   142
D22V11, 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    15   0
  12P GAIN WILD-TYPE 468   9
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                477 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  9 
$`12P GAIN MUTATED`
TCGA-2A-A8W3 TCGA-FC-A4JI TCGA-HC-8264 TCGA-HC-A9TE TCGA-J9-A8CL TCGA-KK-A8I7 
       28.37        28.83         1.58        19.30        13.32        65.82 
TCGA-V1-A9OA TCGA-VP-A875 TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8SO TCGA-YL-A8SQ 
       20.91        75.91        21.80        37.25       114.38        68.48 
TCGA-YL-A9WH TCGA-ZG-A9L0 TCGA-ZG-A9LB 
       14.04        11.67        19.17 

$`12P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
        3.68        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-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-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       18.84        27.75       109.25        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        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.62        10.55        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-A7FD 
       19.96        44.35        43.66        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        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
       74.27       101.79        21.96        31.79        32.91        63.48 
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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       94.36        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         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        25.18        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       119.38       109.58       102.90        23.93        89.49 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        58.32        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        12.36        37.05        48.03 
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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         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        75.75        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-A8SP TCGA-YL-A8SR TCGA-YL-A9WI 
       45.86        46.29        32.45        77.79         8.98        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        70.22        24.33        49.91        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        42.81        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        29.85        22.59        20.28        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 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.58               0.76 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            114.38             165.17 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             21.80              30.84 
[1] "1.6 - 114.4 (21.8)" "0.8 - 165.2 (30.8)"
[1] "hr="     "2.7e+07"
D23V2, continuous
                    vv
clus                  T2  T3  T4
  12P GAIN MUTATED     0  15   0
  12P GAIN WILD-TYPE 187 273  10
D23V3, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T2                0                187
  T3               15                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"
D23V4, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     7   5
  12P GAIN WILD-TYPE 336  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7    5
  12P GAIN WILD-TYPE  336   72
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                7                336
  1                5                 72
[1] 2 2
[1] FALSE
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     9   4
  12P GAIN WILD-TYPE 381  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      9    4
  12P GAIN WILD-TYPE  381   55
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 9                381
  YES                4                 55
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    15   0
  12P GAIN WILD-TYPE 463  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     15    0
  12P GAIN WILD-TYPE  463   14
                                        clus
vv                                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  15                463
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED     4  10   1   0
  12P GAIN WILD-TYPE 309 134   4  15
D23V7, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0                4                309
  R1               10                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"
D23V8, continuous
D23V9, continuous
D23V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       0                         0     0
  12P GAIN WILD-TYPE     2                         7   146
D23V11, multiclass

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    18   0
  12Q GAIN WILD-TYPE 465   9
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                474 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  9 
$`12Q GAIN MUTATED`
TCGA-2A-A8W3 TCGA-CH-5762 TCGA-EJ-A7NH TCGA-FC-A4JI TCGA-HC-8264 TCGA-HC-A9TE 
       28.37        44.02        15.58        28.83         1.58        19.30 
TCGA-J9-A8CL TCGA-KK-A8I7 TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8SO TCGA-YL-A8SQ 
       13.32        65.82        21.80        37.25       114.38        68.48 
TCGA-YL-A9WH TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LU TCGA-ZG-A9LY 
       14.04        11.67        29.85        19.17        19.04        12.16 

$`12Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
        3.68        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        0.92        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
       11.61         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-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        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        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        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        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        35.44        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        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        27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH 
        4.41         4.93         9.53        25.48        18.84        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK 
       13.55        27.12        13.87         5.85        10.62        10.55 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       21.96        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       35.44         6.64        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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 
       25.18        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 
      119.38        75.91       109.58       102.90        23.93        89.49 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        58.32        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        12.36        37.05        48.03 
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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         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        75.75        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-A8SP TCGA-YL-A8SR TCGA-YL-A9WI 
       45.86        46.29        32.45        77.79         8.98        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        70.22        24.33        49.91        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        42.81        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-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 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.58               0.76 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            114.38             165.17 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            20.550             30.855 
[1] "1.6 - 114.4 (20.6)" "0.8 - 165.2 (30.9)"
[1] "hr="     "2.7e+07"
D24V2, continuous
                    vv
clus                  T2  T3  T4
  12Q GAIN MUTATED     1  16   1
  12Q GAIN WILD-TYPE 186 272   9
D24V3, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T2                1                186
  T3               16                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"
D24V4, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     9   6
  12Q GAIN WILD-TYPE 334  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      9    6
  12Q GAIN WILD-TYPE  334   71
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                9                334
  1                6                 71
[1] 2 2
[1] FALSE
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    10   6
  12Q GAIN WILD-TYPE 380  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     10    6
  12Q GAIN WILD-TYPE  380   53
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                10                380
  YES                6                 53
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    18   0
  12Q GAIN WILD-TYPE 460  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     18    0
  12Q GAIN WILD-TYPE  460   14
                                        clus
vv                                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  18                460
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED     3  14   1   0
  12Q GAIN WILD-TYPE 310 130   4  15
D24V7, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                3                310
  R1               14                130
  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"
D24V8, continuous
D24V9, continuous
D24V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       0                         0     1
  12Q GAIN WILD-TYPE     2                         7   145
D24V11, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5753         TCGA-CH-5763         TCGA-CH-5764 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5790         TCGA-CH-5791 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7123         TCGA-EJ-7791 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-HC-7233         TCGA-HC-7748 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7821         TCGA-CH-5737         TCGA-CH-5738 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5739         TCGA-CH-5740         TCGA-CH-5741 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5743         TCGA-CH-5744         TCGA-CH-5746 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5748         TCGA-CH-5750         TCGA-CH-5751 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5752         TCGA-CH-5754         TCGA-CH-5761 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5788         TCGA-CH-5789         TCGA-CH-5792 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5527 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7125         TCGA-EJ-7314 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7321 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7327         TCGA-EJ-7328         TCGA-EJ-7330 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7331         TCGA-EJ-7781         TCGA-EJ-7782 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7783         TCGA-EJ-7784         TCGA-EJ-7785 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7786         TCGA-EJ-7788         TCGA-EJ-7789 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-FC-7961 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         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-7736         TCGA-HC-7737 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7749         TCGA-HC-7750         TCGA-HC-7752 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7818         TCGA-HC-7819         TCGA-HC-7820 
"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 475   9
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                484 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                  9 
$`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       119.38        75.75        62.14 
TCGA-ZG-A9L5 TCGA-ZG-A9N3 
       29.85        11.47 

$`13Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.87        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.96        27.91        30.97        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        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        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85        10.62        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       21.86         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        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        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
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-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       61.68        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       49.02        51.45        48.72        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        77.79        68.48         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        70.22        24.33        49.91        36.10 
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-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       42.81        37.94        36.43        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 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              8.65               0.76 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            119.38             165.17 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            41.390             30.645 
[1] "8.7 - 119.4 (41.4)" "0.8 - 165.2 (30.6)"
[1] "hr="     "2.9e+07"
D25V2, continuous
                    vv
clus                  T2  T3  T4
  13Q GAIN MUTATED     3   4   1
  13Q GAIN WILD-TYPE 184 284   9
D25V3, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T2                3                184
  T3                4                284
  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 338  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    2
  13Q GAIN WILD-TYPE  338   75
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                5                338
  1                2                 75
[1] 2 2
[1] FALSE
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     8   0
  13Q GAIN WILD-TYPE 382  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      8    0
  13Q GAIN WILD-TYPE  382   59
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 8                382
  YES                0                 59
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     7   1
  13Q GAIN WILD-TYPE 471  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7    1
  13Q GAIN WILD-TYPE  471   13
                                        clus
vv                                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   7                471
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED     4   4   0   0
  13Q GAIN WILD-TYPE 309 140   5  15
D25V7, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                4                309
  R1                4                140
  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"
D25V8, continuous
D25V9, continuous
D25V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         0     1
  13Q GAIN WILD-TYPE     2                         7   145
D25V11, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5753         TCGA-CH-5763         TCGA-CH-5764 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5790         TCGA-CH-5791 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7123         TCGA-EJ-7791 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-HC-7233         TCGA-HC-7748 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7821         TCGA-CH-5737         TCGA-CH-5738 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5739         TCGA-CH-5740         TCGA-CH-5741 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5743         TCGA-CH-5744         TCGA-CH-5746 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5748         TCGA-CH-5750         TCGA-CH-5751 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5752         TCGA-CH-5754         TCGA-CH-5761 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5765         TCGA-CH-5766 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5788         TCGA-CH-5789 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-7115         TCGA-EJ-7125 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7785 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7786         TCGA-EJ-7788         TCGA-EJ-7789 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-FC-7961 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         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-7736         TCGA-HC-7737 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7749         TCGA-HC-7750         TCGA-HC-7752 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7818         TCGA-HC-7819         TCGA-HC-7820 
"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     9   1
  14Q GAIN WILD-TYPE 474   8
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                10                482 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                  8 
$`14Q GAIN MUTATED`
TCGA-CH-5772 TCGA-FC-A4JI TCGA-G9-A9S0 TCGA-HC-A631 TCGA-KK-A59Z TCGA-KK-A6E8 
       15.98        28.83        26.01         1.78        86.40        58.19 
TCGA-VP-A872 TCGA-YL-A8SK TCGA-ZG-A9L1 TCGA-ZG-A9LB 
      119.38        46.29        42.81        19.17 

$`14Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
        1.02        12.00         1.02        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        28.18 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        22.36         0.76 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       19.30        27.75       109.25        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        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        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-A6DY 
        8.88        11.57       113.10        83.34        64.70       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
      113.33        90.74        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-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
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-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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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 
       75.75        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        53.06        45.86        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       77.79        68.48         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 
       70.22        24.33        49.91        36.10         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-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       29.85        22.59        20.28        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 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.78               0.76 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            119.38             165.17 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            35.820             30.645 
[1] "1.8 - 119.4 (35.8)" "0.8 - 165.2 (30.6)"
[1] "hr=" "2.5"
D26V2, continuous
                    vv
clus                  T2  T3  T4
  14Q GAIN MUTATED     3   7   0
  14Q GAIN WILD-TYPE 184 281  10
D26V3, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T2                3                184
  T3                7                281
  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   3
  14Q GAIN WILD-TYPE 337  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6    3
  14Q GAIN WILD-TYPE  337   74
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                6                337
  1                3                 74
[1] 2 2
[1] FALSE
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     4   5
  14Q GAIN WILD-TYPE 386  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    5
  14Q GAIN WILD-TYPE  386   54
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 4                386
  YES                5                 54
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     9   1
  14Q GAIN WILD-TYPE 469  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      9    1
  14Q GAIN WILD-TYPE  469   13
                                        clus
vv                                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   9                469
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED     3   6   0   1
  14Q GAIN WILD-TYPE 310 138   5  14
D26V7, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                3                310
  R1                6                138
  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"
D26V8, continuous
D26V9, continuous
D26V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0     1
  14Q GAIN WILD-TYPE     2                         7   145
D26V11, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5753         TCGA-CH-5763         TCGA-CH-5764 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-EJ-5542 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7791         TCGA-G9-6364 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7233         TCGA-HC-7748         TCGA-HC-7821 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        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-5754         TCGA-CH-5761         TCGA-CH-5762 
"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-5792 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5527 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7125         TCGA-EJ-7314 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7321 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7327         TCGA-EJ-7328         TCGA-EJ-7330 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7331         TCGA-EJ-7781         TCGA-EJ-7782 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7783         TCGA-EJ-7784         TCGA-EJ-7785 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7786         TCGA-EJ-7788         TCGA-EJ-7789 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-FC-7961 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         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-7736         TCGA-HC-7737 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7749         TCGA-HC-7750         TCGA-HC-7752 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7818         TCGA-HC-7819         TCGA-HC-7820 
"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 477   9
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                486 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 0                  9 
$`15Q GAIN MUTATED`
TCGA-EJ-5514 TCGA-G9-7525 TCGA-HC-8266 TCGA-V1-A8WV TCGA-VP-A875 TCGA-XK-AAIV 
       60.13        32.68        15.55        22.55        75.91        37.25 

$`15Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       56.98        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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        35.44 
TCGA-G9-7523 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       28.18        26.01        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A4ZV 
       17.95        22.32         1.58        15.88        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-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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        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        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
        5.85        10.62        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        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        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
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-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 
       61.68        64.04        30.38        15.58        35.44         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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        75.75        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        77.79        68.48         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        70.22        24.33        49.91        36.10 
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-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        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 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             15.55               0.76 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             75.91             165.17 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            34.965             30.545 
[1] "15.6 - 75.9 (35.0)" "0.8 - 165.2 (30.5)"
[1] "hr="     "9100000"
D27V2, continuous
                    vv
clus                  T2  T3  T4
  15Q GAIN MUTATED     2   4   0
  15Q GAIN WILD-TYPE 185 284  10
D27V3, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T2                2                185
  T3                4                284
  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 339  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4    2
  15Q GAIN WILD-TYPE  339   75
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                4                339
  1                2                 75
[1] 2 2
[1] FALSE
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     5   1
  15Q GAIN WILD-TYPE 385  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      5    1
  15Q GAIN WILD-TYPE  385   58
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 5                385
  YES                1                 58
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     6   0
  15Q GAIN WILD-TYPE 472  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6    0
  15Q GAIN WILD-TYPE  472   14
                                        clus
vv                                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   6                472
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     4   2   0   0
  15Q GAIN WILD-TYPE 309 142   5  15
D27V7, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                4                309
  R1                2                142
  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"
D27V8, continuous
D27V9, continuous
D27V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         0     1
  15Q GAIN WILD-TYPE     2                         7   145
D27V11, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5753         TCGA-CH-5763         TCGA-CH-5764 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5790         TCGA-CH-5791 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7123         TCGA-EJ-7791 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-HC-7233         TCGA-HC-7748 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7821         TCGA-CH-5737         TCGA-CH-5738 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5739         TCGA-CH-5740         TCGA-CH-5741 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5743         TCGA-CH-5744         TCGA-CH-5746 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5748         TCGA-CH-5750         TCGA-CH-5751 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5752         TCGA-CH-5754         TCGA-CH-5761 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5765         TCGA-CH-5766 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5788         TCGA-CH-5789 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5515         TCGA-EJ-5516 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5527 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7125         TCGA-EJ-7314 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7321 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7327         TCGA-EJ-7328         TCGA-EJ-7330 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7331         TCGA-EJ-7781         TCGA-EJ-7782 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7783         TCGA-EJ-7784         TCGA-EJ-7785 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7786         TCGA-EJ-7788         TCGA-EJ-7789 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-FC-7961 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         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-7736         TCGA-HC-7737 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7749         TCGA-HC-7750         TCGA-HC-7752 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7818         TCGA-HC-7819         TCGA-HC-7820 
"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    32   0
  16P GAIN WILD-TYPE 451   9
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                32                460 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  9 
$`16P GAIN MUTATED`
TCGA-KK-A7B4 TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-7328 TCGA-EJ-7783 TCGA-G9-6373 
       32.45        35.01         0.92        27.68        25.87        26.66 
TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-7232 TCGA-HC-7742 TCGA-HC-A8CY TCGA-HI-7168 
       30.97        40.08        38.17        30.84         9.53       109.25 
TCGA-J9-A52B TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8IF TCGA-KK-A8IK TCGA-QU-A6IL 
       13.87        74.27        65.82        26.43        67.46         3.19 
TCGA-QU-A6IO TCGA-V1-A8WV TCGA-V1-A9O7 TCGA-V1-A9ZI TCGA-VP-A872 TCGA-XK-AAIV 
      122.17        22.55        82.16        53.92       119.38        37.25 
TCGA-YL-A8HM TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WX TCGA-ZG-A9L1 TCGA-ZG-A9L9 
       48.72        77.79        14.04        49.91        42.81        20.28 
TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       11.47         4.34 

$`16P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
        6.44        29.56         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5762 
       24.03         1.02        13.02        31.00         2.04        44.02 
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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       26.99         9.99         2.99        29.00        48.56        57.86 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        56.55        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        46.92        30.31        45.40        47.90        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 
       25.35        33.83        27.09        30.35         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       35.28        38.37        25.68        38.70        36.03        28.24 
TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.33        45.90         3.75        42.94        32.32        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       18.41        21.90         7.56        11.61         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        28.83        22.36        17.23        25.94        20.25 
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        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 
       64.01        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-G9-7522 
       64.18        50.73        52.93        38.96        27.91        35.44 
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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        32.91 
TCGA-HC-7231 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
       30.87        36.26        35.84        31.69        23.57        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        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        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        1.25         4.41         4.93        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       27.75        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.55        27.12         5.85        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 
       49.94        43.69        34.95        36.13       101.79        21.96 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG 
       31.79        32.91        63.48        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        62.96        16.21 
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-A6IN TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
       18.84         5.69       140.19        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        30.38        15.58 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       35.44         6.64        63.52        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZK TCGA-V1-A9ZR 
       28.73        27.19        17.75        49.87        45.47        44.75 
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        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78        16.31        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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 
       75.75        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-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
      114.38        68.48         8.98        53.36        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       24.33        36.10         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-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 
       22.75        17.98        14.96        13.48 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.92               0.76 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            122.17             165.17 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             33.73              30.38 
[1] "0.9 - 122.2 (33.7)" "0.8 - 165.2 (30.4)"
[1] "hr="     "9.4e+07"
D28V2, continuous
                    vv
clus                  T2  T3  T4
  16P GAIN MUTATED     3  28   1
  16P GAIN WILD-TYPE 184 260   9
D28V3, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T2                3                184
  T3               28                260
  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    17  12
  16P GAIN WILD-TYPE 326  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     17   12
  16P GAIN WILD-TYPE  326   65
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               17                326
  1               12                 65
[1] 2 2
[1] FALSE
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    23   6
  16P GAIN WILD-TYPE 367  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     23    6
  16P GAIN WILD-TYPE  367   53
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                23                367
  YES                6                 53
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    31   1
  16P GAIN WILD-TYPE 447  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     31    1
  16P GAIN WILD-TYPE  447   13
                                        clus
vv                                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  31                447
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    17  15   0   0
  16P GAIN WILD-TYPE 296 129   5  15
D28V7, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               17                296
  R1               15                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"
D28V8, continuous
D28V9, continuous
D28V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       0                         0     9
  16P GAIN WILD-TYPE     2                         7   137
D28V11, 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     7   0
  16Q GAIN WILD-TYPE 476   9
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                485 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 0                  9 
$`16Q GAIN MUTATED`
TCGA-CH-5761 TCGA-EJ-7328 TCGA-G9-6373 TCGA-HC-7232 TCGA-QU-A6IL TCGA-YL-A9WH 
        0.92        27.68        26.66        38.17         3.19        14.04 
TCGA-ZG-A9NI 
        4.34 

$`16Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        2.04        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        30.35 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       38.01        40.31        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        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        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       19.30        27.75       109.25        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        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        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        83.34        64.70        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        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        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        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        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       29.23        18.84         5.69       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 
       30.38        15.58        22.55        35.44         6.64        63.52 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       82.16        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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        75.75        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        77.79        68.48         8.98 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        70.22        24.33        49.91        36.10 
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-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        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               0.76 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             38.17             165.17 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             14.04              30.84 
[1] "0.9 - 38.2 (14.0)"  "0.8 - 165.2 (30.8)"
[1] "hr="     "3300000"
D29V2, continuous
                    vv
clus                  T2  T3  T4
  16Q GAIN MUTATED     1   6   0
  16Q GAIN WILD-TYPE 186 282  10
D29V3, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T2                1                186
  T3                6                282
  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     4   1
  16Q GAIN WILD-TYPE 339  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    1
  16Q GAIN WILD-TYPE  339   76
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                4                339
  1                1                 76
[1] 2 2
[1] FALSE
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     5   1
  16Q GAIN WILD-TYPE 385  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5    1
  16Q GAIN WILD-TYPE  385   58
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 5                385
  YES                1                 58
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     7   0
  16Q GAIN WILD-TYPE 471  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      7    0
  16Q GAIN WILD-TYPE  471   14
                                        clus
vv                                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   7                471
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED     5   2   0   0
  16Q GAIN WILD-TYPE 308 142   5  15
D29V7, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                5                308
  R1                2                142
  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"
D29V8, continuous
D29V9, continuous
D29V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         0     4
  16Q GAIN WILD-TYPE     2                         7   142
D29V11, 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     8   0
  17P GAIN WILD-TYPE 475   9
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                484 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                  9 
$`17P GAIN MUTATED`
TCGA-2A-A8VT TCGA-EJ-5527 TCGA-HC-8216 TCGA-TP-A8TT TCGA-V1-A8WV TCGA-V1-A8WW 
       45.14        58.45        22.42        17.29        22.55        35.44 
TCGA-XK-AAIV TCGA-YL-A9WY 
       37.25        36.10 

$`17P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       32.19        20.42        55.92        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 
       74.93        68.35        61.87        36.66        62.76        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87        27.85        30.38        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        15.55        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-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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        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        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
        5.85        10.62        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        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        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
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-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12         0.89        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       64.04        30.38        15.58         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58       102.90 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        89.49        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 
       58.32        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 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
        2.99        31.99        31.96        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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 
       75.75        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        77.79        68.48         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        70.22        24.33        49.91         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       13.28        10.13         4.27        11.67        42.81        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 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             17.29               0.76 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             58.45             165.17 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            35.770             30.545 
[1] "17.3 - 58.5 (35.8)" "0.8 - 165.2 (30.5)"
[1] "hr="     "9100000"
D30V2, continuous
                    vv
clus                  T2  T3  T4
  17P GAIN MUTATED     0   7   1
  17P GAIN WILD-TYPE 187 281   9
D30V3, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T2                0                187
  T3                7                281
  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   5
  17P GAIN WILD-TYPE 340  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    5
  17P GAIN WILD-TYPE  340   72
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                3                340
  1                5                 72
[1] 2 2
[1] FALSE
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     5   3
  17P GAIN WILD-TYPE 385  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    3
  17P GAIN WILD-TYPE  385   56
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 5                385
  YES                3                 56
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     8   0
  17P GAIN WILD-TYPE 470  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      8    0
  17P GAIN WILD-TYPE  470   14
                                        clus
vv                                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   8                470
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     5   3   0   0
  17P GAIN WILD-TYPE 308 141   5  15
D30V7, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                5                308
  R1                3                141
  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"
D30V8, continuous
D30V9, continuous
D30V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       0                         0     1
  17P GAIN WILD-TYPE     2                         7   145
D30V11, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5753         TCGA-CH-5763         TCGA-CH-5764 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5790         TCGA-CH-5791 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7123         TCGA-EJ-7791 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-HC-7233         TCGA-HC-7748 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7821         TCGA-CH-5737         TCGA-CH-5738 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5739         TCGA-CH-5740         TCGA-CH-5741 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5743         TCGA-CH-5744         TCGA-CH-5746 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5748         TCGA-CH-5750         TCGA-CH-5751 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5752         TCGA-CH-5754         TCGA-CH-5761 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5765         TCGA-CH-5766 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5788         TCGA-CH-5789 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7125         TCGA-EJ-7314 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7321 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7327         TCGA-EJ-7328         TCGA-EJ-7330 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7331         TCGA-EJ-7781         TCGA-EJ-7782 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7783         TCGA-EJ-7784         TCGA-EJ-7785 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7786         TCGA-EJ-7788         TCGA-EJ-7789 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-FC-7961 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         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-7736         TCGA-HC-7737 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7749         TCGA-HC-7750         TCGA-HC-7752 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7818         TCGA-HC-7819         TCGA-HC-7820 
"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    11   0
  17Q GAIN WILD-TYPE 472   9
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                11                481 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                  9 
$`17Q GAIN MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-EJ-5527 TCGA-G9-7521 TCGA-HC-8216 TCGA-KK-A8I6 
       45.14        11.51        58.45        30.97        22.42        21.96 
TCGA-TP-A8TT TCGA-V1-A8WV TCGA-V1-A8WW TCGA-XK-AAIV TCGA-YL-A9WY 
       17.29        22.55        35.44        37.25        36.10 

$`17Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       32.19        20.42        55.92        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       28.37        44.84        41.82        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-5754 TCGA-CH-5761 
        1.02        13.02        35.01        31.00         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        61.87        36.66        62.76        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        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        35.28        38.37        25.87        25.68        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
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-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
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        28.83        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       25.94        20.25        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        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        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        35.44        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        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 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       18.18        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        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-A7FD 
       19.96        44.35        43.66        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        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
       74.27       101.79        65.82        31.79        32.91        63.48 
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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
        0.89        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        30.38        15.58 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03 
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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         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        75.75        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        77.79        68.48 
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        70.22        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-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        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 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             11.51               0.76 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             58.45             165.17 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             30.97              30.58 
[1] "11.5 - 58.5 (31.0)" "0.8 - 165.2 (30.6)"
[1] "hr="     "9200000"
D31V2, continuous
                    vv
clus                  T2  T3  T4
  17Q GAIN MUTATED     0  10   1
  17Q GAIN WILD-TYPE 187 278   9
D31V3, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T2                0                187
  T3               10                278
  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   6
  17Q GAIN WILD-TYPE 338  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    6
  17Q GAIN WILD-TYPE  338   71
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                5                338
  1                6                 71
[1] 2 2
[1] FALSE
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     8   3
  17Q GAIN WILD-TYPE 382  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      8    3
  17Q GAIN WILD-TYPE  382   56
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 8                382
  YES                3                 56
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    11   0
  17Q GAIN WILD-TYPE 467  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     11    0
  17Q GAIN WILD-TYPE  467   14
                                        clus
vv                                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  11                467
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED     7   4   0   0
  17Q GAIN WILD-TYPE 306 140   5  15
D31V7, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                7                306
  R1                4                140
  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"
D31V8, continuous
D31V9, continuous
D31V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         0     1
  17Q GAIN WILD-TYPE     2                         7   145
D31V11, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5753         TCGA-CH-5763         TCGA-CH-5764 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5790         TCGA-CH-5791 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7123         TCGA-EJ-7791 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-HC-7233         TCGA-HC-7748 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7821         TCGA-CH-5737         TCGA-CH-5738 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5739         TCGA-CH-5740         TCGA-CH-5741 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5743         TCGA-CH-5744         TCGA-CH-5746 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5748         TCGA-CH-5750         TCGA-CH-5751 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5752         TCGA-CH-5754         TCGA-CH-5761 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5765         TCGA-CH-5766 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5788         TCGA-CH-5789 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7125         TCGA-EJ-7314 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7321 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7327         TCGA-EJ-7328         TCGA-EJ-7330 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7331         TCGA-EJ-7781         TCGA-EJ-7782 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7783         TCGA-EJ-7784         TCGA-EJ-7785 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7786         TCGA-EJ-7788         TCGA-EJ-7789 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-FC-7961 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         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-7736         TCGA-HC-7737 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7749         TCGA-HC-7750         TCGA-HC-7752 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7818         TCGA-HC-7819         TCGA-HC-7820 
"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    18   1
  18P GAIN WILD-TYPE 465   8
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                19                473 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                  8 
$`18P GAIN MUTATED`
TCGA-EJ-5495 TCGA-EJ-5527 TCGA-FC-A4JI TCGA-G9-6329 TCGA-G9-6499 TCGA-G9-7521 
       57.86        58.45        28.83        41.62        50.73        30.97 
TCGA-HC-7742 TCGA-HC-8216 TCGA-HI-7171 TCGA-J9-A52E TCGA-KK-A8I4 TCGA-V1-A8WL 
       30.84        22.42        43.69        10.62        74.27        64.04 
TCGA-VP-A875 TCGA-XK-AAJT TCGA-YL-A9WY TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9M4 
       75.91        47.15        36.10         4.27        42.81        17.98 
TCGA-ZG-A9N3 
       11.47 

$`18P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       29.00        48.56        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 
       74.93        68.35        61.87        36.66        62.76        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       25.94        20.25        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        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        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-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.44        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       31.69        23.57        17.46        23.70        24.59        23.80 
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-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        28.27        23.87        27.85        30.38        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        15.55        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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        88.24 
TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       82.92        20.19        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
        5.85        10.55        13.32        15.22        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        83.34        64.70        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        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        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       36.13       101.79        21.96        65.82        31.79        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-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        67.46        20.65        62.96        16.21 
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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN 
       58.88        16.70        14.73        39.29        61.68        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       36.95        51.81         4.80        25.32        32.61        17.29 
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        75.75 
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 
       77.79        68.48         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       70.22        24.33        49.91         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-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-A9ND TCGA-ZG-A9NI 
       12.16        22.75        14.96        13.48         4.34 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              4.27               0.76 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             75.91             165.17 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             41.62              30.38 
[1] "4.3 - 75.9 (41.6)"  "0.8 - 165.2 (30.4)"
[1] "hr=" "3.5"
D32V2, continuous
                    vv
clus                  T2  T3  T4
  18P GAIN MUTATED     1  17   1
  18P GAIN WILD-TYPE 186 271   9
D32V3, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T2                1                186
  T3               17                271
  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     9   8
  18P GAIN WILD-TYPE 334  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      9    8
  18P GAIN WILD-TYPE  334   69
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                9                334
  1                8                 69
[1] 2 2
[1] FALSE
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    17   2
  18P GAIN WILD-TYPE 373  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     17    2
  18P GAIN WILD-TYPE  373   57
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                17                373
  YES                2                 57
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    19   0
  18P GAIN WILD-TYPE 459  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     19    0
  18P GAIN WILD-TYPE  459   14
                                        clus
vv                                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  19                459
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    11   8   0   0
  18P GAIN WILD-TYPE 302 136   5  15
D32V7, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               11                302
  R1                8                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"
D32V8, continuous
D32V9, continuous
D32V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         0     6
  18P GAIN WILD-TYPE     2                         7   140
D32V11, multiclass
                           clus
vv                          18P GAIN MUTATED 18P 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(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     9   1
  18Q GAIN WILD-TYPE 474   8
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                482 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                  8 
$`18Q GAIN MUTATED`
TCGA-EJ-5527 TCGA-G9-6499 TCGA-HC-8216 TCGA-HI-7171 TCGA-J9-A52E TCGA-KK-A8I4 
       58.45        50.73        22.42        43.69        10.62        74.27 
TCGA-V1-A8WL TCGA-VP-A875 TCGA-ZG-A9L1 TCGA-ZG-A9M4 
       64.04        75.91        42.81        17.98 

$`18Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87        27.85        30.38        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        15.55        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-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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        88.24        82.92 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        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-A7FD 
       19.96        44.35        43.66        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        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        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        57.67        49.94        43.69        34.95        36.13 
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-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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WS 
       16.70        14.73        39.29        61.68        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       22.55        35.44         6.64        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         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        25.18        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       119.38       109.58       102.90        23.93        89.49 
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        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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        75.75 
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 
       77.79        68.48         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 
       70.22        24.33        49.91        36.10         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-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 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             10.62               0.76 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             75.91             165.17 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            47.210             30.445 
[1] "10.6 - 75.9 (47.2)" "0.8 - 165.2 (30.4)"
[1] "hr=" "5.8"
D33V2, continuous
                    vv
clus                  T2  T3  T4
  18Q GAIN MUTATED     0  10   0
  18Q GAIN WILD-TYPE 187 278  10
D33V3, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T2                0                187
  T3               10                278
  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     7   3
  18Q GAIN WILD-TYPE 336  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    3
  18Q GAIN WILD-TYPE  336   74
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                7                336
  1                3                 74
[1] 2 2
[1] FALSE
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     9   1
  18Q GAIN WILD-TYPE 381  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      9    1
  18Q GAIN WILD-TYPE  381   58
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 9                381
  YES                1                 58
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    10   0
  18Q GAIN WILD-TYPE 468  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     10    0
  18Q GAIN WILD-TYPE  468   14
                                        clus
vv                                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  10                468
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     6   4   0   0
  18Q GAIN WILD-TYPE 307 140   5  15
D33V7, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                6                307
  R1                4                140
  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"
D33V8, continuous
D33V9, continuous
D33V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0     3
  18Q GAIN WILD-TYPE     2                         7   143
D33V11, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q 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(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    12   0
  19P GAIN WILD-TYPE 471   9
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                12                480 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  9 
$`19P GAIN MUTATED`
TCGA-KK-A7B4 TCGA-CH-5751 TCGA-HC-7213 TCGA-HC-A9TE TCGA-KK-A8ID TCGA-V1-A8WV 
       32.45        35.01        40.08        19.30        69.27        22.55 
TCGA-VP-A875 TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A9WL TCGA-ZG-A9L5 TCGA-ZG-A9N3 
       75.91        75.75        56.52        24.33        29.85        11.47 

$`19P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
        6.44        29.56         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-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-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       18.84        27.75       109.25        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        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        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        83.34        64.70        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        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        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
       32.91        63.48        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        67.46        20.65        62.96        16.21 
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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       30.38        15.58        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       62.14        60.56        16.83        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        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       68.48         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
        4.27        11.67        42.81        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-A9ND TCGA-ZG-A9NI 
       12.16        22.75        17.98        14.96        13.48         4.34 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             11.47               0.76 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             75.91             165.17 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            33.730             30.545 
[1] "11.5 - 75.9 (33.7)" "0.8 - 165.2 (30.5)"
[1] "hr="     "9300000"
D34V2, continuous
                    vv
clus                  T2  T3  T4
  19P GAIN MUTATED     0  10   2
  19P GAIN WILD-TYPE 187 278   8
D34V3, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T2                0                187
  T3               10                278
  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     6   6
  19P GAIN WILD-TYPE 337  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6    6
  19P GAIN WILD-TYPE  337   71
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                6                337
  1                6                 71
[1] 2 2
[1] FALSE
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    10   2
  19P GAIN WILD-TYPE 380  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     10    2
  19P GAIN WILD-TYPE  380   57
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                10                380
  YES                2                 57
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    12   0
  19P GAIN WILD-TYPE 466  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     12    0
  19P GAIN WILD-TYPE  466   14
                                        clus
vv                                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  12                466
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED     4   8   0   0
  19P GAIN WILD-TYPE 309 136   5  15
D34V7, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                4                309
  R1                8                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"
D34V8, continuous
D34V9, continuous
D34V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       0                         0     2
  19P GAIN WILD-TYPE     2                         7   144
D34V11, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                153 
        TCGA-CH-5753         TCGA-CH-5763         TCGA-CH-5764 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5790         TCGA-CH-5791 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7123         TCGA-EJ-7791 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-HC-7233         TCGA-HC-7748 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7821         TCGA-CH-5737         TCGA-CH-5738 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5739         TCGA-CH-5740         TCGA-CH-5741 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5743         TCGA-CH-5744         TCGA-CH-5746 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5748         TCGA-CH-5750         TCGA-CH-5752 
"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-5765         TCGA-CH-5766         TCGA-CH-5767 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5788         TCGA-CH-5789         TCGA-CH-5792 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5527 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7125         TCGA-EJ-7314 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7321 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7327         TCGA-EJ-7328         TCGA-EJ-7330 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7331         TCGA-EJ-7781         TCGA-EJ-7782 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7783         TCGA-EJ-7784         TCGA-EJ-7785 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7786         TCGA-EJ-7788         TCGA-EJ-7789 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-FC-7961 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         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-7736         TCGA-HC-7737         TCGA-HC-7738 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7740         TCGA-HC-7742         TCGA-HC-7744 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7745         TCGA-HC-7747         TCGA-HC-7749 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         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    12   0
  19Q GAIN WILD-TYPE 471   9
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                12                480 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  9 
$`19Q GAIN MUTATED`
TCGA-KK-A7B4 TCGA-CH-5751 TCGA-HC-7213 TCGA-HC-A9TE TCGA-HI-7168 TCGA-KK-A8ID 
       32.45        35.01        40.08        19.30       109.25        69.27 
TCGA-V1-A8WV TCGA-VP-A875 TCGA-YL-A8HO TCGA-YL-A8SB TCGA-ZG-A9L5 TCGA-ZG-A9N3 
       22.55        75.91        75.75        56.52        29.85        11.47 

$`19Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
        6.44        29.56         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-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-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        27.75        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       18.18        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        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-A7FD 
       19.96        44.35        43.66        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        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       63.48        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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        35.44         6.64        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         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        25.18        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       119.38       109.58       102.90        23.93        89.49 
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        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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-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-A8SQ 
       45.86        46.29        32.45       114.38        77.79        68.48 
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        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
        4.27        11.67        42.81        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-A9ND TCGA-ZG-A9NI 
       12.16        22.75        17.98        14.96        13.48         4.34 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             11.47               0.76 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            109.25             165.17 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            37.545             30.445 
[1] "11.5 - 109.2 (37.5)" "0.8 - 165.2 (30.4)" 
[1] "hr="     "2.6e+07"
D35V2, continuous
                    vv
clus                  T2  T3  T4
  19Q GAIN MUTATED     0  10   2
  19Q GAIN WILD-TYPE 187 278   8
D35V3, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T2                0                187
  T3               10                278
  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     6   6
  19Q GAIN WILD-TYPE 337  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6    6
  19Q GAIN WILD-TYPE  337   71
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                6                337
  1                6                 71
[1] 2 2
[1] FALSE
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    11   1
  19Q GAIN WILD-TYPE 379  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     11    1
  19Q GAIN WILD-TYPE  379   58
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                11                379
  YES                1                 58
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    12   0
  19Q GAIN WILD-TYPE 466  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     12    0
  19Q GAIN WILD-TYPE  466   14
                                        clus
vv                                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  12                466
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED     4   8   0   0
  19Q GAIN WILD-TYPE 309 136   5  15
D35V7, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                4                309
  R1                8                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"
D35V8, continuous
D35V9, continuous
D35V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       0                         0     3
  19Q GAIN WILD-TYPE     2                         7   143
D35V11, 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    25   1
  20P GAIN WILD-TYPE 458   8
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                26                466 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                  8 
$`20P GAIN MUTATED`
TCGA-J9-A8CN TCGA-KC-A7FA TCGA-4L-AA1F TCGA-EJ-A65M TCGA-G9-6499 TCGA-HC-A9TE 
       40.67        19.66        11.51         7.56        50.73        19.30 
TCGA-HI-7168 TCGA-J9-A52E TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A8I4 TCGA-KK-A8IF 
      109.25        10.62        58.19        49.94        74.27        26.43 
TCGA-V1-A9O5 TCGA-V1-A9OL TCGA-VP-A875 TCGA-VP-A87D TCGA-XJ-A83H TCGA-XK-AAIV 
       63.52        62.89        75.91        60.92        42.08        37.25 
TCGA-XQ-A8TA TCGA-YL-A8HM TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A9LU TCGA-ZG-A9LZ 
        4.80        48.72        14.04        53.36        19.04        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       17.98        11.47 

$`20P GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-KK-A7AP TCGA-KK-A7B3 
       31.43         3.48         7.00        32.61         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       44.84        41.82        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-5754 TCGA-CH-5761 TCGA-CH-5762 
       13.02        35.01        31.00         2.04         0.92        44.02 
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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       26.99         9.99         2.99        29.00        48.56        57.86 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        56.55        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        46.92        30.31        45.40        47.90        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        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        35.28        38.37        25.87        25.68        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
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-A65F TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A7NF 
       12.92        13.71        18.41        21.90        11.61         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        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        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        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        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        35.44        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        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 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH 
        4.41         4.93         9.53        25.48        18.84        27.75 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AQ 
       67.59       115.13        68.15       113.33        90.74        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B1 
       58.36        27.02        34.65        57.67        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       36.13       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       63.48        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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55        35.44         6.64        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       20.91        38.93        79.00        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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 
       25.18        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 
      119.38       109.58       102.90        23.93        89.49        55.56 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI 
       45.47        32.19        12.36        37.05        48.03        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TB TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       17.29         4.87        52.96        49.02        51.45        75.75 
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-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       77.79        68.48         8.98        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        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-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        14.96        13.48         4.34 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              4.80               0.76 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            109.25             165.17 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            38.960             30.545 
[1] "4.8 - 109.2 (39.0)" "0.8 - 165.2 (30.5)"
[1] "hr=" "2.8"
D36V2, continuous
                    vv
clus                  T2  T3  T4
  20P GAIN MUTATED     3  21   1
  20P GAIN WILD-TYPE 184 267   9
D36V3, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T2                3                184
  T3               21                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"
D36V4, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    15   8
  20P GAIN WILD-TYPE 328  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     15    8
  20P GAIN WILD-TYPE  328   69
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               15                328
  1                8                 69
[1] 2 2
[1] FALSE
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    18   6
  20P GAIN WILD-TYPE 372  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     18    6
  20P GAIN WILD-TYPE  372   53
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                18                372
  YES                6                 53
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    26   0
  20P GAIN WILD-TYPE 452  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     26    0
  20P GAIN WILD-TYPE  452   14
                                        clus
vv                                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  26                452
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED    12  11   0   1
  20P GAIN WILD-TYPE 301 133   5  14
D36V7, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               12                301
  R1               11                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"
D36V8, continuous
D36V9, continuous
D36V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       0                         0     2
  20P GAIN WILD-TYPE     2                         7   144
D36V11, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                153 
        TCGA-CH-5753         TCGA-CH-5763         TCGA-CH-5764 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5790         TCGA-CH-5791 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7123         TCGA-EJ-7791 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-HC-7233         TCGA-HC-7748 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7821         TCGA-CH-5737         TCGA-CH-5738 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5739         TCGA-CH-5740         TCGA-CH-5741 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5743         TCGA-CH-5744         TCGA-CH-5746 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5748         TCGA-CH-5750         TCGA-CH-5751 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5752         TCGA-CH-5754         TCGA-CH-5761 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5765         TCGA-CH-5766 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5788         TCGA-CH-5789 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-7115         TCGA-EJ-7125 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7792         TCGA-EJ-7793 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7794         TCGA-EJ-7797         TCGA-FC-7708 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FC-7961         TCGA-G9-6329         TCGA-G9-6332 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6333         TCGA-G9-6336         TCGA-G9-6338 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6342         TCGA-G9-6343         TCGA-G9-6348 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6351         TCGA-G9-6353         TCGA-G9-6356 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6361         TCGA-G9-6362         TCGA-G9-6363 
"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-7736         TCGA-HC-7737 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7749         TCGA-HC-7750         TCGA-HC-7752 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7818         TCGA-HC-7819         TCGA-HC-7820 
"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    29   0
  20Q GAIN WILD-TYPE 454   9
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                29                463 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  9 
$`20Q GAIN MUTATED`
TCGA-J9-A8CN TCGA-4L-AA1F TCGA-CH-5762 TCGA-EJ-5518 TCGA-EJ-7314 TCGA-EJ-A65M 
       40.67        11.51        44.02        69.63        37.81         7.56 
TCGA-G9-6494 TCGA-G9-6499 TCGA-HC-A9TE TCGA-HI-7168 TCGA-J9-A52E TCGA-KK-A6E8 
       58.22        50.73        19.30       109.25        10.62        58.19 
TCGA-KK-A8I4 TCGA-KK-A8IF TCGA-V1-A9O5 TCGA-V1-A9OL TCGA-VP-A875 TCGA-VP-A87D 
       74.27        26.43        63.52        62.89        75.91        60.92 
TCGA-XJ-A83H TCGA-XK-AAIV TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A9WH TCGA-YL-A9WI 
       42.08        37.25        48.72        62.14        14.04        53.36 
TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       12.43        19.04        22.75        17.98        11.47 

$`20Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-KC-A7FA TCGA-KK-A7AP 
       31.43         3.48         7.00        32.61        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       28.37        44.84        41.82        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-5754 TCGA-CH-5761 
        1.02        13.02        35.01        31.00         2.04         0.92 
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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       26.99         9.99         2.99        29.00        48.56        57.86 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        56.55        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        46.92        30.31        45.40        47.90        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        62.10        64.50        74.93        68.35        61.87 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        62.76        58.45        60.23        41.85        60.10 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       88.34        93.70        83.57        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       27.09        30.35        27.68         6.28        24.39        35.28 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        38.70        36.03        28.24 
TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.33        45.90         3.75        42.94        32.32        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       18.41        21.90        11.61         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 
       28.83        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
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-G9-6496 TCGA-G9-6498 
       37.97        58.45        25.15        27.29        56.75        64.18 
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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        27.75        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        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        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-A7FD 
       19.96        44.35        43.66        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        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
      113.33        90.74        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-A8I5 
       57.67        49.94        43.69        34.95        36.13       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
       21.96        65.82        31.79        32.91        63.48        67.43 
TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       69.27        82.36        66.18       113.98        51.25        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       35.44         6.64        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       79.00        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H 
      102.90        23.93        89.49        55.56        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       58.32        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 
       12.36        37.05        48.03        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-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S9 
        4.87        52.96        49.02        51.45        75.75        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        77.79        68.48 
TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
        8.98        60.99        70.22        24.33        49.91        36.10 
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-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND 
       19.17         3.78        16.96        12.16        14.96        13.48 
TCGA-ZG-A9NI 
        4.34 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              7.56               0.76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            109.25             165.17 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             42.08              30.38 
[1] "7.6 - 109.2 (42.1)" "0.8 - 165.2 (30.4)"
[1] "hr="     "2.7e+07"
D37V2, continuous
                    vv
clus                  T2  T3  T4
  20Q GAIN MUTATED     3  23   3
  20Q GAIN WILD-TYPE 184 265   7
D37V3, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T2                3                184
  T3               23                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"
D37V4, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    18   9
  20Q GAIN WILD-TYPE 325  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     18    9
  20Q GAIN WILD-TYPE  325   68
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               18                325
  1                9                 68
[1] 2 2
[1] FALSE
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    21   7
  20Q GAIN WILD-TYPE 369  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     21    7
  20Q GAIN WILD-TYPE  369   52
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                21                369
  YES                7                 52
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    29   0
  20Q GAIN WILD-TYPE 449  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     29    0
  20Q GAIN WILD-TYPE  449   14
                                        clus
vv                                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  29                449
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED    12  15   0   1
  20Q GAIN WILD-TYPE 301 129   5  14
D37V7, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               12                301
  R1               15                129
  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"
D37V8, continuous
D37V9, continuous
D37V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       0                         0     6
  20Q GAIN WILD-TYPE     2                         7   140
D37V11, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q 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(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    21   0
  21Q GAIN WILD-TYPE 462   9
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                471 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                  9 
$`21Q GAIN MUTATED`
TCGA-KK-A7B4 TCGA-EJ-7784 TCGA-G9-6499 TCGA-HC-A9TE TCGA-HI-7168 TCGA-J9-A52E 
       32.45        25.68        50.73        19.30       109.25        10.62 
TCGA-KK-A59Z TCGA-KK-A8I4 TCGA-KK-A8IA TCGA-V1-A8WV TCGA-V1-A9Z7 TCGA-VP-A872 
       86.40        74.27        63.48        22.55        28.73       119.38 
TCGA-VP-A875 TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A9WH 
       75.91        21.80        37.25        75.75        62.14        14.04 
TCGA-YL-A9WI TCGA-ZG-A9L0 TCGA-ZG-A9LB 
       53.36        11.67        19.17 

$`21Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
        6.44        29.56         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-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-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        27.75        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK 
       18.18        13.55        27.12        13.87         5.85        10.55 
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-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        83.34        64.70       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 
       49.94        43.69        34.95        36.13       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       65.82        31.79        32.91        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        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 
       61.68        64.04        30.38        15.58        35.44         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 
       62.89        12.20        15.65        37.28        35.08        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         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        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       44.91        25.78        16.31       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       89.49        55.56        60.92        66.97        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        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-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S9 TCGA-YL-A8SA 
       52.96        49.02        51.45        48.72        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        77.79        68.48         8.98 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        70.22        24.33        49.91        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        42.81        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        29.85        22.59        20.28        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 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             10.62               0.76 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            119.38             165.17 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             37.25              30.51 
[1] "10.6 - 119.4 (37.2)" "0.8 - 165.2 (30.5)" 
[1] "hr="     "7.8e+07"
D38V2, continuous
                    vv
clus                  T2  T3  T4
  21Q GAIN MUTATED     2  19   0
  21Q GAIN WILD-TYPE 185 269  10
D38V3, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T2                2                185
  T3               19                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"
D38V4, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    13   8
  21Q GAIN WILD-TYPE 330  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     13    8
  21Q GAIN WILD-TYPE  330   69
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               13                330
  1                8                 69
[1] 2 2
[1] FALSE
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    19   2
  21Q GAIN WILD-TYPE 371  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     19    2
  21Q GAIN WILD-TYPE  371   57
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                19                371
  YES                2                 57
[1] 2 2
[1] FALSE
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    20   1
  21Q GAIN WILD-TYPE 458  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     20    1
  21Q GAIN WILD-TYPE  458   13
                                        clus
vv                                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  20                458
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    10   9   1   1
  21Q GAIN WILD-TYPE 303 135   4  14
D38V7, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               10                303
  R1                9                135
  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"
D38V8, continuous
D38V9, continuous
D38V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         0     3
  21Q GAIN WILD-TYPE     2                         7   143
D38V11, 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 479   9
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                488 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  9 
$`22Q GAIN MUTATED`
TCGA-EJ-5514 TCGA-VP-A876 TCGA-ZG-A9L0 TCGA-ZG-A9LZ 
       60.13       109.58        11.67        22.75 

$`22Q GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       56.98        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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        35.44 
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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
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        27.85        30.38 
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        15.55 
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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       27.12        13.87         5.85        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
       21.96        65.82        31.79        32.91        63.48        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 
       67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       22.55        35.44         6.64        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         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        25.18        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       16.31       119.38        75.91       102.90        23.93        89.49 
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        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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        75.75 
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 
       77.79        68.48         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 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        42.81        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-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       16.96        19.04        12.16        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             11.67               0.76 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            109.58             165.17 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            41.440             30.645 
[1] "11.7 - 109.6 (41.4)" "0.8 - 165.2 (30.6)" 
[1] "hr="     "3300000"
D39V2, continuous
                    vv
clus                  T2  T3  T4
  22Q GAIN MUTATED     2   2   0
  22Q GAIN WILD-TYPE 185 286  10
D39V3, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T2                2                185
  T3                2                286
  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 340  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    1
  22Q GAIN WILD-TYPE  340   76
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                3                340
  1                1                 76
[1] 2 2
[1] FALSE
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3   1
  22Q GAIN WILD-TYPE 387  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    1
  22Q GAIN WILD-TYPE  387   58
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 3                387
  YES                1                 58
[1] 2 2
[1] FALSE
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     4   0
  22Q GAIN WILD-TYPE 474  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    0
  22Q GAIN WILD-TYPE  474   14
                                        clus
vv                                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   4                474
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED     2   2   0   0
  22Q GAIN WILD-TYPE 311 142   5  15
D39V7, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                2                311
  R1                2                142
  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"
D39V8, continuous
D39V9, continuous
D39V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         0     1
  22Q GAIN WILD-TYPE     2                         7   145
D39V11, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5753         TCGA-CH-5763         TCGA-CH-5764 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5790         TCGA-CH-5791 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7123         TCGA-EJ-7791 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-HC-7233         TCGA-HC-7748 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7821         TCGA-CH-5737         TCGA-CH-5738 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5739         TCGA-CH-5740         TCGA-CH-5741 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5743         TCGA-CH-5744         TCGA-CH-5746 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5748         TCGA-CH-5750         TCGA-CH-5751 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5752         TCGA-CH-5754         TCGA-CH-5761 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5765         TCGA-CH-5766 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5788         TCGA-CH-5789 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5515         TCGA-EJ-5516 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5527 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7125         TCGA-EJ-7314 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7321 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7327         TCGA-EJ-7328         TCGA-EJ-7330 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7331         TCGA-EJ-7781         TCGA-EJ-7782 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7783         TCGA-EJ-7784         TCGA-EJ-7785 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7786         TCGA-EJ-7788         TCGA-EJ-7789 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-FC-7961 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         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-7736         TCGA-HC-7737 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7749         TCGA-HC-7750         TCGA-HC-7752 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HC-7818         TCGA-HC-7819         TCGA-HC-7820 
"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     7   0
  XP GAIN WILD-TYPE 476   9
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                7               485 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 9 
$`XP GAIN MUTATED`
TCGA-HC-A4ZV TCGA-J9-A8CM TCGA-VP-A87H TCGA-XK-AAJA TCGA-YL-A8S8 TCGA-ZG-A9L1 
        0.76        15.22        21.80        30.58        62.14        42.81 
TCGA-ZG-A9L5 
       29.85 

$`XP GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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 
       28.83        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
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 
       35.44        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       15.55        22.36         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       27.12        13.87         5.85        10.62        10.55        13.32 
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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       35.44         6.64        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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 
       25.18        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 
      119.38        75.91       109.58       102.90        23.93        89.49 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        58.32        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        12.36        37.05        48.03 
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-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       37.25        40.04        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        51.45        48.72        75.75        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        77.79        68.48         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        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       11.67        37.94        36.43        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 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.76              0.89 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            62.14            165.17 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            29.85             30.81 
[1] "0.8 - 62.1 (29.9)"  "0.9 - 165.2 (30.8)"
[1] "hr="     "9100000"
D40V2, continuous
                   vv
clus                 T2  T3  T4
  XP GAIN MUTATED     0   6   1
  XP GAIN WILD-TYPE 187 282   9
D40V3, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T2               0               187
  T3               6               282
  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   3
  XP GAIN WILD-TYPE 339  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      4    3
  XP GAIN WILD-TYPE  339   74
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               4               339
  1               3                74
[1] 2 2
[1] FALSE
D40V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     5   1
  XP GAIN WILD-TYPE 385  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      5    1
  XP GAIN WILD-TYPE  385   58
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                5               385
  YES               1                58
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     7   0
  XP GAIN WILD-TYPE 471  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    0
  XP GAIN WILD-TYPE  471   14
                                        clus
vv                                       XP GAIN MUTATED XP GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  7               471
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED     1   5   1   0
  XP GAIN WILD-TYPE 312 139   4  15
D40V7, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0               1               312
  R1               5               139
  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"
D40V8, continuous
D40V9, continuous
D40V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         0     0
  XP GAIN WILD-TYPE     2                         7   146
D40V11, multiclass

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     7   0
  XQ GAIN WILD-TYPE 476   9
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               485 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 9 
$`XQ GAIN MUTATED`
TCGA-HC-A4ZV TCGA-J9-A8CM TCGA-VP-A87H TCGA-XK-AAJA TCGA-YL-A8S8 TCGA-ZG-A9L1 
        0.76        15.22        21.80        30.58        62.14        42.81 
TCGA-ZG-A9L5 
       29.85 

$`XQ GAIN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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 
       28.83        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
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 
       35.44        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       15.55        22.36         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       27.12        13.87         5.85        10.62        10.55        13.32 
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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       35.44         6.64        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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 
       25.18        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 
      119.38        75.91       109.58       102.90        23.93        89.49 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        58.32        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        12.36        37.05        48.03 
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-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       37.25        40.04        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        51.45        48.72        75.75        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        77.79        68.48         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        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       11.67        37.94        36.43        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 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.76              0.89 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            62.14            165.17 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            29.85             30.81 
[1] "0.8 - 62.1 (29.9)"  "0.9 - 165.2 (30.8)"
[1] "hr="     "9100000"
D41V2, continuous
                   vv
clus                 T2  T3  T4
  XQ GAIN MUTATED     0   6   1
  XQ GAIN WILD-TYPE 187 282   9
D41V3, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T2               0               187
  T3               6               282
  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   3
  XQ GAIN WILD-TYPE 339  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4    3
  XQ GAIN WILD-TYPE  339   74
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               4               339
  1               3                74
[1] 2 2
[1] FALSE
D41V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     5   1
  XQ GAIN WILD-TYPE 385  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5    1
  XQ GAIN WILD-TYPE  385   58
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                5               385
  YES               1                58
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     7   0
  XQ GAIN WILD-TYPE 471  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      7    0
  XQ GAIN WILD-TYPE  471   14
                                        clus
vv                                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  7               471
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED     1   5   1   0
  XQ GAIN WILD-TYPE 312 139   4  15
D41V7, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               1               312
  R1               5               139
  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"
D41V8, continuous
D41V9, continuous
D41V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         0     0
  XQ GAIN WILD-TYPE     2                         7   146
D41V11, multiclass

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    22   0
  1P LOSS WILD-TYPE 461   9
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               22               470 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                 9 
$`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       109.25        13.32        86.40 
TCGA-KK-A6E0 TCGA-KK-A6E6 TCGA-KK-A8IG TCGA-KK-A8IK TCGA-M7-A725 TCGA-V1-A8WV 
       48.76       113.33        82.36        67.46        18.84        22.55 
TCGA-V1-A8WW TCGA-VP-AA1N TCGA-YL-A8SJ TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WL 
       35.44        44.88        45.86        68.48        14.04        24.33 
TCGA-ZG-A9KY TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LZ 
        4.27        20.28        12.43        22.75 

$`1P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.87        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        47.15 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       18.84        19.30        27.75        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        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.62        10.55        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-A7FD 
       19.96        44.35        43.66        21.86         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 
       11.57       113.10        83.34        64.70       141.21        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 
      165.17        67.59       115.13        68.15        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM 
       26.43        66.18       113.98        51.25        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       29.23         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       30.38        15.58         6.64        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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        75.75 
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-A8SO TCGA-YL-A8SP 
       28.77        53.06        46.29        32.45       114.38        77.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY 
        8.98        53.36        60.99        70.22        49.91        36.10 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L1 
        3.09        14.53        13.28        10.13        11.67        42.81 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LN 
       37.94        36.43        29.85        22.59        19.17         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-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             4.27              0.76 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           113.33            165.17 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           37.760            30.545 
[1] "4.3 - 113.3 (37.8)" "0.8 - 165.2 (30.5)"
[1] "hr="     "2.6e+07"
D42V2, continuous
                   vv
clus                 T2  T3  T4
  1P LOSS MUTATED     3  18   1
  1P LOSS WILD-TYPE 184 270   9
D42V3, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T2               3               184
  T3              18               270
  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   6
  1P LOSS WILD-TYPE 328  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     15    6
  1P LOSS WILD-TYPE  328   71
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              15               328
  1               6                71
[1] 2 2
[1] FALSE
D42V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    15   6
  1P LOSS WILD-TYPE 375  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     15    6
  1P LOSS WILD-TYPE  375   53
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               15               375
  YES               6                53
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    22   0
  1P LOSS WILD-TYPE 456  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     22    0
  1P LOSS WILD-TYPE  456   14
                                        clus
vv                                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 22               456
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    12  10   0   0
  1P LOSS WILD-TYPE 301 134   5  15
D42V7, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              12               301
  R1              10               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"
D42V8, continuous
D42V9, continuous
D42V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       0                         0     4
  1P LOSS WILD-TYPE     2                         7   142
D42V11, 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 477   9
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6               486 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                 9 
$`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        68.48        20.28        12.43 

$`1Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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 
       28.83        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
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        64.01        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        35.44 
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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
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        27.85        30.38 
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        15.55 
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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       61.68        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03 
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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       37.25        40.04        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         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        75.75        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        77.79 
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        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       22.59        19.17         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 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            12.43              0.76 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            82.36            165.17 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           33.400            30.645 
[1] "12.4 - 82.4 (33.4)" "0.8 - 165.2 (30.6)"
[1] "hr="     "9100000"
D43V2, continuous
                   vv
clus                 T2  T3  T4
  1Q LOSS MUTATED     0   6   0
  1Q LOSS WILD-TYPE 187 282  10
D43V3, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T2               0               187
  T3               6               282
  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 340  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    2
  1Q LOSS WILD-TYPE  340   75
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               3               340
  1               2                75
[1] 2 2
[1] FALSE
D43V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     4   1
  1Q LOSS WILD-TYPE 386  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4    1
  1Q LOSS WILD-TYPE  386   58
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                4               386
  YES               1                58
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     6   0
  1Q LOSS WILD-TYPE 472  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6    0
  1Q LOSS WILD-TYPE  472   14
                                        clus
vv                                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  6               472
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED     1   5   0   0
  1Q LOSS WILD-TYPE 312 139   5  15
D43V7, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               1               312
  R1               5               139
  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"
D43V8, continuous
D43V9, continuous
D43V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0     1
  1Q LOSS WILD-TYPE     2                         7   145
D43V11, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1               154 
       TCGA-CH-5753        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-EJ-5542        TCGA-EJ-7123 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7791        TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7821        TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5752        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-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5788        TCGA-CH-5789 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-7115        TCGA-EJ-7125 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"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-G9-6365 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075        TCGA-HC-7077 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7081 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7820        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    13   1
  2P LOSS WILD-TYPE 470   8
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               478 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                 8 
$`2P LOSS MUTATED`
TCGA-HC-A76W TCGA-HC-7213 TCGA-HC-7749 TCGA-J9-A8CL TCGA-KK-A6E4 TCGA-KK-A6E5 
        7.00        40.08        23.80        13.32       115.13        68.15 
TCGA-VP-A875 TCGA-XK-AAJT TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A9WK TCGA-ZG-A9L0 
       75.91        47.15        75.75        45.86        70.22        11.67 
TCGA-ZG-A9L5 TCGA-ZG-A9LZ 
       29.85        22.75 

$`2P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
       31.43         3.48        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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        35.44 
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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 
       30.84        17.46        23.70        24.59        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        27.85        30.38        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        15.55        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-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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        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        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
        5.85        10.62        10.55        15.22        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        83.34        64.70        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E6 
      141.21        48.76        72.26       165.17        67.59       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       90.74        58.19        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-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
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-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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       36.95        51.81         4.80        25.32        32.61        17.29 
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-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        77.79        68.48 
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 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       42.81        37.94        36.43        22.59        20.28        19.17 
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 
             7.00              0.76 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           115.13            165.17 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           42.970            30.545 
[1] "7.0 - 115.1 (43.0)" "0.8 - 165.2 (30.5)"
[1] "hr=" "2"  
D44V2, continuous
                   vv
clus                 T2  T3  T4
  2P LOSS MUTATED     1  12   1
  2P LOSS WILD-TYPE 186 276   9
D44V3, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T2               1               186
  T3              12               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"
D44V4, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    11   2
  2P LOSS WILD-TYPE 332  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     11    2
  2P LOSS WILD-TYPE  332   75
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              11               332
  1               2                75
[1] 2 2
[1] FALSE
D44V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    11   1
  2P LOSS WILD-TYPE 379  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     11    1
  2P LOSS WILD-TYPE  379   58
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               11               379
  YES               1                58
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    14   0
  2P LOSS WILD-TYPE 464  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     14    0
  2P LOSS WILD-TYPE  464   14
                                        clus
vv                                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 14               464
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     6   8   0   0
  2P LOSS WILD-TYPE 307 136   5  15
D44V7, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               6               307
  R1               8               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"
D44V8, continuous
D44V9, continuous
D44V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0     2
  2P LOSS WILD-TYPE     2                         7   144
D44V11, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               153 
       TCGA-CH-5753        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-EJ-5542        TCGA-EJ-7123 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7791        TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7821        TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5752        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-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5788        TCGA-CH-5789 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-7115        TCGA-EJ-7125 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"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-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7820        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 466   8
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               474 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                 8 
$`2Q LOSS MUTATED`
TCGA-HC-A76W TCGA-KK-A7B3 TCGA-HC-7213 TCGA-HC-7749 TCGA-HC-8266 TCGA-J9-A8CL 
        7.00        29.56        40.08        23.80        15.55        13.32 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A8IK TCGA-VP-A875 TCGA-XK-AAJT TCGA-YL-A8HO 
      115.13        68.15        67.46        75.91        47.15        75.75 
TCGA-YL-A8SJ TCGA-YL-A9WK TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LZ 
       45.86        70.22        11.67        29.85        19.17        22.75 

$`2Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
       31.43         3.48        32.61        40.67        19.66         6.44 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       17.46        23.70        24.59        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        27.85        30.38        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-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       18.18        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       10.55        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        83.34        64.70        86.40       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       72.26       165.17        67.59       113.33        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       61.68        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       119.38 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XQ-A8TA 
       40.04        30.58        41.39        36.95        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         4.87        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-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        53.06        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        77.79        68.48         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       60.99        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        42.81        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       22.59        20.28        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        17.98        14.96        11.47        13.48         4.34 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             7.00              0.76 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           115.13            165.17 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           34.965            30.645 
[1] "7.0 - 115.1 (35.0)" "0.8 - 165.2 (30.6)"
[1] "hr=" "1.7"
D45V2, continuous
                   vv
clus                 T2  T3  T4
  2Q LOSS MUTATED     2  15   1
  2Q LOSS WILD-TYPE 185 273   9
D45V3, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T2               2               185
  T3              15               273
  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 328  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     15    2
  2Q LOSS WILD-TYPE  328   75
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              15               328
  1               2                75
[1] 2 2
[1] FALSE
D45V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    15   1
  2Q LOSS WILD-TYPE 375  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     15    1
  2Q LOSS WILD-TYPE  375   58
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               15               375
  YES               1                58
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    18   0
  2Q LOSS WILD-TYPE 460  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     18    0
  2Q LOSS WILD-TYPE  460   14
                                        clus
vv                                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 18               460
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     8  10   0   0
  2Q LOSS WILD-TYPE 305 134   5  15
D45V7, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               8               305
  R1              10               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"
D45V8, continuous
D45V9, continuous
D45V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0     2
  2Q LOSS WILD-TYPE     2                         7   144
D45V11, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               153 
       TCGA-CH-5753        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-EJ-5542        TCGA-EJ-7123 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7791        TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7821        TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5752        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-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5788        TCGA-CH-5789 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-7115        TCGA-EJ-7125 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"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-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7820        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 474   9
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9               483 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                 9 
$`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        72.26       113.33        15.58        82.16 
TCGA-VP-A876 TCGA-YL-A8SQ TCGA-ZG-A9N3 
      109.58        68.48        11.47 

$`3P LOSS WILD-TYPE`
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
       12.00         1.02        15.98        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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        35.44 
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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        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        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85        10.62        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       64.70        86.40       141.21        48.76       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
      115.13        68.15        90.74        58.19        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        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        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        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 
       64.04        30.38        22.55        35.44         6.64        63.52 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38        75.91       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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 
       75.75        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        77.79         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 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       13.28        10.13         4.27        11.67        42.81        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-A9ND TCGA-ZG-A9NI 
       14.96        13.48         4.34 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.02              0.76 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           113.33            165.17 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            68.48             30.58 
[1] "1.0 - 113.3 (68.5)" "0.8 - 165.2 (30.6)"
[1] "hr="     "9400000"
D46V2, continuous
                   vv
clus                 T2  T3  T4
  3P LOSS MUTATED     1   8   0
  3P LOSS WILD-TYPE 186 280  10
D46V3, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T2               1               186
  T3               8               280
  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 338  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    3
  3P LOSS WILD-TYPE  338   74
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               5               338
  1               3                74
[1] 2 2
[1] FALSE
D46V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     6   2
  3P LOSS WILD-TYPE 384  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6    2
  3P LOSS WILD-TYPE  384   57
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                6               384
  YES               2                57
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     9   0
  3P LOSS WILD-TYPE 469  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      9    0
  3P LOSS WILD-TYPE  469   14
                                        clus
vv                                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  9               469
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED     4   4   0   1
  3P LOSS WILD-TYPE 309 140   5  14
D46V7, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               4               309
  R1               4               140
  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"
D46V8, continuous
D46V9, continuous
D46V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         0     1
  3P LOSS WILD-TYPE     2                         7   145
D46V11, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1               154 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772        TCGA-CH-5790 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-EJ-5542        TCGA-EJ-7123        TCGA-EJ-7791 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748        TCGA-HC-7821 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       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-5765 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5771        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5792 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5532        TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7314 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        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-G9-6365 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075        TCGA-HC-7077 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7081 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7820        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 478   9
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5               487 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 9 
$`3Q LOSS MUTATED`
TCGA-G9-7523 TCGA-KK-A6E6 TCGA-V1-A9O7 TCGA-VP-A876 TCGA-YL-A8SQ 
       28.18       113.33        82.16       109.58        68.48 

$`3Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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 
       28.83        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
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 
       35.44        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
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        27.85        30.38 
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        15.55 
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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       27.12        13.87         5.85        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 
      165.17        67.59       115.13        68.15        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       35.44         6.64        63.52        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       119.38 
TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       75.91       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         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        75.75        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-A8SR 
       45.86        46.29        32.45       114.38        77.79         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        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        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 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            28.18              0.76 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           113.33            165.17 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            82.16             30.51 
[1] "28.2 - 113.3 (82.2)" "0.8 - 165.2 (30.5)" 
[1] "hr="     "9300000"
D47V2, continuous
                   vv
clus                 T2  T3  T4
  3Q LOSS MUTATED     1   4   0
  3Q LOSS WILD-TYPE 186 284  10
D47V3, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T2               1               186
  T3               4               284
  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 338  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    0
  3Q LOSS WILD-TYPE  338   77
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               5               338
  1               0                77
[1] 2 2
[1] FALSE
D47V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     4   1
  3Q LOSS WILD-TYPE 386  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    1
  3Q LOSS WILD-TYPE  386   58
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                4               386
  YES               1                58
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5   0
  3Q LOSS WILD-TYPE 473  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    0
  3Q LOSS WILD-TYPE  473   14
                                        clus
vv                                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  5               473
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED     2   3   0   0
  3Q LOSS WILD-TYPE 311 141   5  15
D47V7, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               2               311
  R1               3               141
  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"
D47V8, continuous
D47V9, continuous
D47V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         0     0
  3Q LOSS WILD-TYPE     2                         7   146
D47V11, multiclass

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    23   0
  4P LOSS WILD-TYPE 460   9
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               469 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                0                 9 
$`4P LOSS MUTATED`
TCGA-CH-5753 TCGA-4L-AA1F TCGA-CH-5754 TCGA-EJ-A65B TCGA-FC-7961 TCGA-HC-A48F 
        1.02        11.51         2.04        23.34        15.42        22.36 
TCGA-J9-A52B TCGA-KK-A59Z TCGA-KK-A6E1 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A8IK 
       13.87        86.40        72.26        90.74        52.93        67.46 
TCGA-V1-A8WW TCGA-V1-A9O5 TCGA-V1-A9OL TCGA-XK-AAJT TCGA-YL-A8HK TCGA-YL-A8SL 
       35.44        63.52        62.89        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-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
       12.00         1.02        15.98        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       28.37        44.84        41.82        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-5761 TCGA-CH-5762 
        1.02        13.02        35.01        31.00         0.92        44.02 
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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       26.99         9.99         2.99        29.00        48.56        57.86 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        56.55        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        46.92        30.31        45.40        47.90        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        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        35.28        38.37        25.87        25.68        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D 
       20.58        17.23        25.74        23.80        21.96        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         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        28.83        22.36        17.23        25.94        20.25 
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        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        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        35.44        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        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 
       27.85        30.38        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        15.55         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.55        27.12         5.85        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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-A6E2 TCGA-KK-A6E3 
       83.34        64.70       141.21        48.76       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A7AU TCGA-KK-A7AV 
      115.13        68.15       113.33        58.19        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        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        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        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        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       38.93        79.00        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03 
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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       37.25        40.04        30.58        41.39        36.95        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        75.75        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-A9WI 
       46.29       114.38        77.79        68.48         8.98        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        70.22        24.33        49.91        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       14.53        13.28        10.13         4.27        11.67        42.81 
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-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 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.02              0.76 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            90.74            165.17 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            23.34             30.71 
[1] "1.0 - 90.7 (23.3)"  "0.8 - 165.2 (30.7)"
[1] "hr="     "2.6e+07"
D48V2, continuous
                   vv
clus                 T2  T3  T4
  4P LOSS MUTATED     4  18   1
  4P LOSS WILD-TYPE 183 270   9
D48V3, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T2               4               183
  T3              18               270
  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"
D48V4, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    11  12
  4P LOSS WILD-TYPE 332  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11   12
  4P LOSS WILD-TYPE  332   65
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              11               332
  1              12                65
[1] 2 2
[1] FALSE
D48V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    15   6
  4P LOSS WILD-TYPE 375  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     15    6
  4P LOSS WILD-TYPE  375   53
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               15               375
  YES               6                53
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    22   1
  4P LOSS WILD-TYPE 456  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     22    1
  4P LOSS WILD-TYPE  456   13
                                        clus
vv                                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 22               456
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               1                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED     8  13   0   1
  4P LOSS WILD-TYPE 305 131   5  14
D48V7, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               8               305
  R1              13               131
  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"
D48V8, continuous
D48V9, continuous
D48V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       0                         0     3
  4P LOSS WILD-TYPE     2                         7   143
D48V11, multiclass
                           clus
vv                          4P LOSS MUTATED 4P 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(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    16   0
  4Q LOSS WILD-TYPE 467   9
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16               476 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 9 
$`4Q LOSS MUTATED`
TCGA-EJ-A65B TCGA-FC-7961 TCGA-G9-6499 TCGA-HC-A48F TCGA-HC-A9TE TCGA-J9-A52B 
       23.34        15.42        50.73        22.36        19.30        13.87 
TCGA-KK-A59Z TCGA-KK-A8IK TCGA-V1-A9O5 TCGA-YL-A8HK TCGA-YL-A8SL TCGA-YL-A9WH 
       86.40        67.46        63.52        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-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 
       22.32         1.58        15.88        15.55         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK 
       18.18        13.55        27.12         5.85        10.62        10.55 
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-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        83.34        64.70       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
       21.96        65.82        31.79        32.91        63.48        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        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       35.44         6.64        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03 
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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       37.25        40.04        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        51.45        48.72        75.75        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-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        46.29       114.38        77.79        68.48         8.98 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        70.22        24.33        49.91        36.10 
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-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB 
       42.81        37.94        36.43        29.85        22.59        19.17 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9N3 
        3.78        16.96        19.04        12.16        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            12.43              0.76 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            86.40            165.17 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           22.555            30.825 
[1] "12.4 - 86.4 (22.6)" "0.8 - 165.2 (30.8)"
[1] "hr="     "9300000"
D49V2, continuous
                   vv
clus                 T2  T3  T4
  4Q LOSS MUTATED     3  12   1
  4Q LOSS WILD-TYPE 184 276   9
D49V3, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T2               3               184
  T3              12               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"
D49V4, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     9   7
  4Q LOSS WILD-TYPE 334  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9    7
  4Q LOSS WILD-TYPE  334   70
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               9               334
  1               7                70
[1] 2 2
[1] FALSE
D49V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    10   6
  4Q LOSS WILD-TYPE 380  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10    6
  4Q LOSS WILD-TYPE  380   53
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               10               380
  YES               6                53
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    15   1
  4Q LOSS WILD-TYPE 463  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     15    1
  4Q LOSS WILD-TYPE  463   13
                                        clus
vv                                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 15               463
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               1                13
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED     5  10   0   0
  4Q LOSS WILD-TYPE 308 134   5  15
D49V7, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0               5               308
  R1              10               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"
D49V8, continuous
D49V9, continuous
D49V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       0                         0     2
  4Q LOSS WILD-TYPE     2                         7   144
D49V11, multiclass
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2               153 
       TCGA-CH-5753        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-EJ-5542        TCGA-EJ-7123 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-7791        TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HC-7821        TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CH-5752        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5788        TCGA-CH-5789 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-7115        TCGA-EJ-7125 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FC-7708        TCGA-G9-6329        TCGA-G9-6332        TCGA-G9-6333 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6365 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7736 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7749 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HC-7820        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HI-7171 
"4Q LOSS WILD-TYPE" 

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    12   0
  5P LOSS WILD-TYPE 471   9
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12               480 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                 9 
$`5P LOSS MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5766 TCGA-HI-7168 TCGA-J9-A52B 
       45.14        11.51        35.01         1.02       109.25        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-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       32.19        20.42        55.92        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       28.37        44.84        41.82        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-5754 TCGA-CH-5761 TCGA-CH-5762 
        1.02        13.02        31.00         2.04         0.92        44.02 
TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 
       23.01        15.06        24.03         2.04        13.02        26.99 
TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
        9.99         2.99        29.00        48.56        57.86        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       46.92        30.31        45.40        47.90        64.60        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       62.04        48.53        56.98        60.13        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        69.63        64.50        74.93        68.35        61.87 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        62.76        58.45        60.23        41.85        60.10 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       88.34        93.70        83.57        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       33.83        27.09        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 
       35.28        38.37        25.87        25.68        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       28.24        36.33        45.90         3.75        42.94        32.32 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       77.16        76.41        38.10        24.85        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         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        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        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        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        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        35.44        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        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        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       19.30        27.75        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK 
       18.18        13.55        27.12         5.85        10.62        10.55 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
       21.96        65.82        31.79        32.91        63.48        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 
       67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       22.55        35.44         6.64        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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        75.75 
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 
       77.79        68.48         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       70.22        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       10.13         4.27        11.67        42.81        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       29.85        22.59        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-A9NI 
       19.04        12.16        17.98        14.96        11.47         4.34 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1.02              0.76 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           109.25            165.17 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           21.515            30.825 
[1] "1.0 - 109.2 (21.5)" "0.8 - 165.2 (30.8)"
[1] "hr="     "9100000"
D50V2, continuous
                   vv
clus                 T2  T3  T4
  5P LOSS MUTATED     0  10   2
  5P LOSS WILD-TYPE 187 278   8
D50V3, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T2               0               187
  T3              10               278
  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 336  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      7    4
  5P LOSS WILD-TYPE  336   73
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               7               336
  1               4                73
[1] 2 2
[1] FALSE
D50V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5   5
  5P LOSS WILD-TYPE 385  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    5
  5P LOSS WILD-TYPE  385   54
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                5               385
  YES               5                54
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    12   0
  5P LOSS WILD-TYPE 466  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     12    0
  5P LOSS WILD-TYPE  466   14
                                        clus
vv                                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 12               466
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED     4   8   0   0
  5P LOSS WILD-TYPE 309 136   5  15
D50V7, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               4               309
  R1               8               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"
D50V8, continuous
D50V9, continuous
D50V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         0     3
  5P LOSS WILD-TYPE     2                         7   143
D50V11, 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    23   0
  5Q LOSS WILD-TYPE 460   9
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23               469 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                0                 9 
$`5Q LOSS MUTATED`
TCGA-KC-A7FA TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5766 
       19.66        45.14        11.51        35.01         0.92         1.02 
TCGA-EJ-5507 TCGA-FC-A4JI TCGA-HC-8266 TCGA-HC-A48F TCGA-HI-7168 TCGA-J9-A52B 
       47.90        28.83        15.55        22.36       109.25        13.87 
TCGA-KK-A8IF TCGA-KK-A8IK TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-VP-AA1N TCGA-YL-A9WI 
       26.43        67.46        22.55        63.52        44.88        53.36 
TCGA-YL-A9WL TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9N3 
       24.33        29.85        20.28        19.17        11.47 

$`5Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP 
       31.43         3.48         7.00        32.61        40.67         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        55.92        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       44.84        41.82        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-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5767 
       13.02        31.00         2.04        44.02        23.01        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       45.40        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 
       17.95        22.32         1.58        15.88         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       19.30        27.75        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK 
       18.18        13.55        27.12         5.85        10.62        10.55 
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        83.34        64.70        86.40       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       90.74        58.19        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-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
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-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        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW 
       39.29        61.68        64.04        30.38        15.58        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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        75.75        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        77.79        68.48         8.98 
TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       14.04        60.99        70.22        49.91        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       14.53        13.28        10.13         4.27        11.67        42.81 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       37.94        36.43        22.59        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND 
       19.04        12.16        22.75        17.98        14.96        13.48 
TCGA-ZG-A9NI 
        4.34 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.92              0.76 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           109.25            165.17 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            24.33             30.84 
[1] "0.9 - 109.2 (24.3)" "0.8 - 165.2 (30.8)"
[1] "hr="     "2.6e+07"
D51V2, continuous
                   vv
clus                 T2  T3  T4
  5Q LOSS MUTATED     2  17   4
  5Q LOSS WILD-TYPE 185 271   6
D51V3, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T2               2               185
  T3              17               271
  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  11
  5Q LOSS WILD-TYPE 332  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11   11
  5Q LOSS WILD-TYPE  332   66
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              11               332
  1              11                66
[1] 2 2
[1] FALSE
D51V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    13   7
  5Q LOSS WILD-TYPE 377  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     13    7
  5Q LOSS WILD-TYPE  377   52
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               13               377
  YES               7                52
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    23   0
  5Q LOSS WILD-TYPE 455  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     23    0
  5Q LOSS WILD-TYPE  455   14
                                        clus
vv                                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 23               455
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    11  12   0   0
  5Q LOSS WILD-TYPE 302 132   5  15
D51V7, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              11               302
  R1              12               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"
D51V8, continuous
D51V9, continuous
D51V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         0     5
  5Q LOSS WILD-TYPE     2                         7   141
D51V11, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS 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(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    25   1
  6P LOSS WILD-TYPE 458   8
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               26               466 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                 8 
$`6P LOSS MUTATED`
TCGA-HC-7821 TCGA-2A-A8VT TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-7784 
       31.43        45.14        47.90        48.53        69.63        25.68 
TCGA-HC-7213 TCGA-HC-A48F TCGA-HC-A632 TCGA-J4-A83J TCGA-J9-A52B TCGA-J9-A8CL 
       40.08        22.36         2.01        22.88        13.87        13.32 
TCGA-KC-A7F6 TCGA-KK-A8IC TCGA-V1-A8MG TCGA-V1-A8WW TCGA-VP-AA1N TCGA-XQ-A8TA 
        8.65        67.43        28.18        35.44        44.88         4.80 
TCGA-YL-A8HO TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A8QW TCGA-ZG-A9L5 
       75.75        68.48        14.04        53.36         3.09        29.85 
TCGA-ZG-A9LB TCGA-ZG-A9LM 
       19.17        12.43 

$`6P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        55.92        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       38.50        45.73        46.92        30.31        45.40        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        62.04        56.98        60.13        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       62.10        64.50        74.93        68.35        61.87        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       93.70        83.57        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       27.09        30.35        27.68         6.28        24.39        35.28 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.87        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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 
       28.83        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
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 
       35.44        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
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        27.85        30.38 
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        15.55 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        0.76         1.78         2.20         1.61        17.42         2.33 
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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        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        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L 
       25.28        27.91        16.83        22.52        10.78        23.67 
TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E 
       17.85        18.18        13.55        27.12         5.85        10.62 
TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       10.55        15.22        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-A6E1 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8ID 
       21.96        65.82        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       20.05        47.64        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       61.68        64.04        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 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TB 
       30.58        41.39        36.95        47.15        51.81        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
      114.38        77.79         8.98        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       49.91        36.10        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        42.81        37.94        36.43        22.59        20.28 
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 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             2.01              0.76 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            75.75            165.17 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           29.015            30.760 
[1] "2.0 - 75.8 (29.0)"  "0.8 - 165.2 (30.8)"
[1] "hr=" "3.1"
D52V2, continuous
                   vv
clus                 T2  T3  T4
  6P LOSS MUTATED     4  18   3
  6P LOSS WILD-TYPE 183 270   7
D52V3, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T2               4               183
  T3              18               270
  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    13  10
  6P LOSS WILD-TYPE 330  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     13   10
  6P LOSS WILD-TYPE  330   67
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              13               330
  1              10                67
[1] 2 2
[1] FALSE
D52V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    19   5
  6P LOSS WILD-TYPE 371  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     19    5
  6P LOSS WILD-TYPE  371   54
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               19               371
  YES               5                54
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    26   0
  6P LOSS WILD-TYPE 452  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     26    0
  6P LOSS WILD-TYPE  452   14
                                        clus
vv                                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 26               452
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    11  13   0   0
  6P LOSS WILD-TYPE 302 131   5  15
D52V7, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              11               302
  R1              13               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"
D52V8, continuous
D52V9, continuous
D52V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       0                         1     5
  6P LOSS WILD-TYPE     2                         6   141
D52V11, 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    39   2
  6Q LOSS WILD-TYPE 444   7
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               41               451 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                 7 
$`6Q LOSS MUTATED`
TCGA-CH-5753 TCGA-HC-7821 TCGA-KC-A7FA TCGA-2A-A8VT TCGA-EJ-5507 TCGA-EJ-5511 
        1.02        31.43        19.66        45.14        47.90        48.53 
TCGA-EJ-5518 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-FC-7961 TCGA-G9-A9S0 
       69.63        38.37        25.68        36.03        15.42        26.01 
TCGA-HC-7078 TCGA-HC-7213 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A9TE TCGA-J4-A83J 
       65.26        40.08        22.36         2.01        19.30        22.88 
TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CL TCGA-KC-A7F6 TCGA-KK-A6E1 TCGA-KK-A8IC 
       13.87        10.62        13.32         8.65        72.26        67.43 
TCGA-V1-A8WW TCGA-VN-A88O TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A9DI TCGA-XK-AAIV 
       35.44        15.81        44.88        45.47        48.03        37.25 
TCGA-XQ-A8TA TCGA-YL-A8HO TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK 
        4.80        75.75        68.48        14.04        53.36        70.22 
TCGA-ZG-A8QW TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9ND 
        3.09        29.85        19.17        12.43        13.48 

$`6Q LOSS WILD-TYPE`
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
       12.00         1.02        15.98        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-A6AQ 
       14.83        28.70        39.39        44.55        26.04         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 
        7.00        32.61        40.67         6.44        29.56        32.45 
TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
        2.73        41.00        41.49        32.19        20.42        55.92 
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        45.30         3.68        28.37        44.84        41.82 
TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 
       20.22        11.51         2.99         6.97        22.06         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       12.99        13.97         1.97        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 
       35.01        31.00         2.04         0.92        44.02        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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
        9.99         2.99        29.00        48.56        57.86        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       46.92        30.31        45.40        64.60        48.13        62.04 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 
       56.98        60.13        60.23        62.10        62.10        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 
       27.68         6.28        24.39        35.28        25.87        38.70 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       28.24        36.33        45.90         3.75        42.94        32.32 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       77.16        76.41        38.10        24.85        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         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        28.83        22.36        17.23        25.94        20.25 
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        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        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        35.44        28.18        32.68        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        69.53        38.93        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        40.14        28.60        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55         0.76 
TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        1.78         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        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 
       40.04        33.01        25.32        30.94        30.81        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-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV 
       16.83        22.52        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP 
       13.55        27.12         5.85        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        83.34        64.70        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
      141.21        48.76       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       63.48        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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        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        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         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        25.18        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 
      119.38        75.91       109.58       102.90        23.93        89.49 
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        58.32        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       14.76        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TB TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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 
       77.79         8.98        60.99        24.33        49.91        36.10 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       14.53        13.28        10.13         4.27        11.67        42.81 
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-A9NI 
        4.34 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1.02              0.76 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            75.75            165.17 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            29.85             30.71 
[1] "1.0 - 75.8 (29.9)"  "0.8 - 165.2 (30.7)"
[1] "hr=" "4.5"
D53V2, continuous
                   vv
clus                 T2  T3  T4
  6Q LOSS MUTATED     7  30   3
  6Q LOSS WILD-TYPE 180 258   7
D53V3, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T2               7               180
  T3              30               258
  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    25  14
  6Q LOSS WILD-TYPE 318  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     25   14
  6Q LOSS WILD-TYPE  318   63
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              25               318
  1              14                63
[1] 2 2
[1] FALSE
D53V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    28  10
  6Q LOSS WILD-TYPE 362  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     28   10
  6Q LOSS WILD-TYPE  362   49
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               28               362
  YES              10                49
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    41   0
  6Q LOSS WILD-TYPE 437  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     41    0
  6Q LOSS WILD-TYPE  437   14
                                        clus
vv                                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 41               437
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    19  17   0   2
  6Q LOSS WILD-TYPE 294 127   5  13
D53V7, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              19               294
  R1              17               127
  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"
D53V8, continuous
D53V9, continuous
D53V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       0                         2     9
  6Q LOSS WILD-TYPE     2                         5   137
D53V11, 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   167   4
  8P LOSS WILD-TYPE 316   5
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              171               321 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                 5 
$`8P LOSS MUTATED`
TCGA-CH-5753 TCGA-CH-5764 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 TCGA-EJ-7325 
        1.02         1.02        32.02        33.01        49.74        35.18 
TCGA-G9-6364 TCGA-HC-7821 TCGA-HC-A6AQ TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP 
       39.39        31.43         3.48        32.61        40.67         6.44 
TCGA-KK-A7B4 TCGA-XK-AAJ3 TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       32.45        41.49        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5739 TCGA-CH-5744 TCGA-CH-5754 
       28.37        41.82        20.22        22.06         1.97         2.04 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5771 TCGA-CH-5788 TCGA-EJ-5499 
       23.01         1.02        15.06        13.02        26.99        46.52 
TCGA-EJ-5501 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-5527 TCGA-EJ-5530 
       44.88        47.90        48.53        69.63        58.45        60.23 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7314 TCGA-EJ-7321 TCGA-EJ-7330 TCGA-EJ-7781 
       60.10        88.34        37.81        27.09         6.28        35.28 
TCGA-EJ-7783 TCGA-EJ-7788 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       25.87        28.24        76.41        38.10        24.85        25.18 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A8FS TCGA-EJ-AB27 TCGA-FC-7708 TCGA-G9-6332 
       12.92        13.71         8.75         4.77        28.41        87.35 
TCGA-G9-6333 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6354 TCGA-G9-6361 
       81.04        83.87        55.76        80.55        67.92        46.52 
TCGA-G9-6369 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6384 TCGA-G9-6494 
       39.95        40.31        26.66        31.50        25.15        58.22 
TCGA-G9-6496 TCGA-G9-7509 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-HC-7077 
       56.75        52.93        26.01        23.93         6.08        69.53 
TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7744 TCGA-HC-7819 TCGA-HC-8216 TCGA-HC-8256 
       40.08        30.87        17.46        17.85        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 
       23.87        22.32         1.58        15.55        22.36         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7170 
        2.20         1.61        19.30        27.75       109.25        82.92 
TCGA-HI-7171 TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67S TCGA-J4-A83I TCGA-J4-AATZ 
       43.69        30.94        30.81        27.39        22.52        13.55 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-KC-A4BV TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KK-A59Y 
       10.62        13.32        43.66         8.65         8.88        64.70 
TCGA-KK-A6E1 TCGA-KK-A6E5 TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A8I5 
       72.26        68.15        27.02        34.65        49.94       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 
       62.96        21.14        18.84         5.69       122.17        18.12 
TCGA-TK-A8OK TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8WL TCGA-V1-A8WS 
        0.89        20.05        28.18        58.88        64.04        15.58 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OL 
       35.44         6.64        82.16        20.91        79.00        62.89 
TCGA-V1-A9ZK TCGA-VN-A88K TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VP-A875 
       45.47        25.51        15.81        41.42        25.78        75.91 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87J TCGA-VP-A87K TCGA-XJ-A83F TCGA-XJ-A83G 
       89.49        55.56        58.32        42.94        37.05        48.03 
TCGA-XJ-A83H TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJP TCGA-XK-AAJR 
       42.08         2.99        31.96        37.25        41.39        36.95 
TCGA-XQ-A8TA TCGA-YJ-A8SW TCGA-YL-A8HK TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SJ 
        4.80         4.87        49.02        41.46        45.14        45.86 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WL 
       32.45        77.79         8.98        14.04        53.36        24.33 
TCGA-YL-A9WX TCGA-ZG-A9L0 TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       49.91        11.67        16.96        12.16        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

$`8P LOSS WILD-TYPE`
TCGA-CH-5763 TCGA-CH-5772 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7791 TCGA-EJ-A46B 
       12.00        15.98        84.56        36.13        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-A76W 
       21.96        14.83        28.70        44.55        26.04         7.00 
TCGA-KC-A7FA TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAK1 TCGA-2A-A8VL 
       19.66        29.56         2.73        41.00        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-AAYF TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 
       55.92        44.84        11.51         2.99         6.97         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
       12.99        13.97        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5789 
       31.00         0.92        44.02        24.03         2.04         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       56.55        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       64.60        48.13        62.04        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        62.10        64.50        74.93        68.35        61.87 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5531 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7315 
       36.66        62.76        41.85        93.70        83.57        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7782 
       25.35        33.83        30.35        27.68        24.39        38.37 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       25.68        38.70        36.03        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       42.94        32.32        77.16        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.80        21.96        23.34        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 
        4.21        10.82         9.27         9.83         4.54         4.31 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       41.62        67.99        66.67        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       50.70        47.15        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6498 
       40.18        38.01        37.97        58.45        27.29        64.18 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.96        27.91        30.97        35.44        28.18 
TCGA-G9-7525 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
       32.68        30.94         3.68        19.76        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       32.91        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       30.84        23.70        24.59        23.80        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8258 TCGA-HC-8259 
       30.51        30.84        24.56        19.36        27.85        30.38 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AO 
       22.55        17.95        15.88         0.76         1.78        17.42 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 
       25.32        27.58        32.05        29.92         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       27.91        16.83        22.88        10.78        23.67        17.85 
TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CM 
       18.18        27.12        13.87         5.85        10.55        15.22 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7F3 
       12.69        30.71        59.67        19.96        44.35        21.86 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       11.57       113.10        83.34        86.40       141.21        48.76 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
      165.17        67.59       115.13       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       52.93        58.36        57.67        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH 
       74.27        65.82        31.79        67.43        69.27        66.18 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 
       51.25        67.46        20.65        16.21        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IP 
       34.85        25.08        29.23         3.19       140.19        86.14 
TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       17.29        47.64        16.70        14.73        39.29        61.68 
TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OQ 
       30.38        22.55        63.52        94.36        38.93        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M 
       49.87        53.92        44.75         8.84        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 
       25.18        44.91        16.31       119.38       109.58       102.90 
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        12.36        48.03         9.04        31.99 
TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TB TCGA-Y6-A8TL 
       40.04        30.58        47.15        51.81        25.32        32.61 
TCGA-Y6-A9XI TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       17.29        52.96        51.45        48.72        75.75        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       60.56        16.83        56.52        28.77        53.06        46.29 
TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A8QW 
      114.38        68.48        60.99        70.22        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        42.81        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-A9LU TCGA-ZG-A9LZ 
        3.78        19.04        22.75 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.89              0.76 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           122.17            165.17 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            30.94             30.38 
[1] "0.9 - 122.2 (30.9)" "0.8 - 165.2 (30.4)"
[1] "hr=" "1.7"
D54V2, continuous
                   vv
clus                 T2  T3  T4
  8P LOSS MUTATED    45 121   3
  8P LOSS WILD-TYPE 142 167   7
D54V3, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T2              45               142
  T3             121               167
  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   115  33
  8P LOSS WILD-TYPE 228  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    115   33
  8P LOSS WILD-TYPE  228   44
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             115               228
  1              33                44
[1] 2 2
[1] FALSE
D54V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   132  21
  8P LOSS WILD-TYPE 258  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    132   21
  8P LOSS WILD-TYPE  258   38
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              132               258
  YES              21                38
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   166   5
  8P LOSS WILD-TYPE 312   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    166    5
  8P LOSS WILD-TYPE  312    9
                                        clus
vv                                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                166               312
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               5                 9
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   105  50   2   8
  8P LOSS WILD-TYPE 208  94   3   7
D54V7, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             105               208
  R1              50                94
  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"
D54V8, continuous
D54V9, continuous
D54V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       2                         3    47
  8P LOSS WILD-TYPE     0                         4    99
D54V11, 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    19   2
  8Q LOSS WILD-TYPE 464   7
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               471 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                 7 
$`8Q LOSS MUTATED`
TCGA-CH-5753 TCGA-CH-5764 TCGA-KK-A7B4 TCGA-2A-A8VT TCGA-CH-5739 TCGA-CH-5754 
        1.02         1.02        32.45        45.14        22.06         2.04 
TCGA-EJ-5507 TCGA-EJ-5527 TCGA-G9-A9S0 TCGA-HC-7744 TCGA-HC-8257 TCGA-HI-7168 
       47.90        58.45        26.01        17.46        23.87       109.25 
TCGA-HI-7171 TCGA-KK-A59Y TCGA-KK-A8IF TCGA-MG-AAMC TCGA-TP-A8TV TCGA-V1-A8WS 
       43.69        64.70        26.43         5.69        20.05        15.58 
TCGA-V1-A9ZK TCGA-YL-A8SF TCGA-YL-A9WI 
       45.47        45.14        53.36 

$`8Q LOSS WILD-TYPE`
TCGA-CH-5763 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 TCGA-EJ-7123 
       12.00        15.98        32.02        33.01        49.74        84.56 
TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J 
       36.13        35.18        36.76        21.60        21.96        14.83 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ 
       28.70        39.39        44.55        26.04        31.43         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 
        7.00        32.61        40.67        19.66         6.44        29.56 
TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
        2.73        41.00        41.49        32.19        20.42        55.92 
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        45.30         3.68        28.37        44.84        41.82 
TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 
       20.22        11.51         2.99         6.97         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
       13.97         1.97        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       31.00         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       45.40        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 
       74.93        68.35        61.87        36.66        62.76        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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        35.44        28.18 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        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-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       27.75        88.24        82.92        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       27.12        13.87         5.85        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       83.34        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        67.43        69.27 
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        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08        29.23        18.84         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12         0.89        17.29        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       30.38        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87        53.92        44.75         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        25.18        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       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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 
       75.75        62.14        60.56        16.83        56.52        41.46 
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 
       77.79        68.48         8.98        14.04        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       10.13         4.27        11.67        42.81        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 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.02              0.76 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           109.25            165.17 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            26.43             30.71 
[1] "1.0 - 109.2 (26.4)" "0.8 - 165.2 (30.7)"
[1] "hr=" "9.6"
D55V2, continuous
                   vv
clus                 T2  T3  T4
  8Q LOSS MUTATED     1  19   1
  8Q LOSS WILD-TYPE 186 269   9
D55V3, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T2               1               186
  T3              19               269
  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"
D55V4, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    11   9
  8Q LOSS WILD-TYPE 332  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     11    9
  8Q LOSS WILD-TYPE  332   68
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              11               332
  1               9                68
[1] 2 2
[1] FALSE
D55V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    12   5
  8Q LOSS WILD-TYPE 378  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     12    5
  8Q LOSS WILD-TYPE  378   54
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               12               378
  YES               5                54
[1] 2 2
[1] FALSE
D55V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    21   0
  8Q LOSS WILD-TYPE 457  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     21    0
  8Q LOSS WILD-TYPE  457   14
                                        clus
vv                                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 21               457
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    11   9   0   1
  8Q LOSS WILD-TYPE 302 135   5  14
D55V7, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              11               302
  R1               9               135
  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"
D55V8, continuous
D55V9, continuous
D55V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         0     9
  8Q LOSS WILD-TYPE     2                         7   137
D55V11, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q 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(56) Variable = 9P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    21   0
  9P LOSS WILD-TYPE 462   9
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               21               471 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                0                 9 
$`9P LOSS MUTATED`
TCGA-KK-A8IB TCGA-4L-AA1F TCGA-CH-5751 TCGA-EJ-5507 TCGA-EJ-5521 TCGA-EJ-7781 
        2.73        11.51        35.01        47.90        74.93        35.28 
TCGA-FC-7961 TCGA-G9-7521 TCGA-HC-8216 TCGA-HC-A631 TCGA-HI-7168 TCGA-J4-A67L 
       15.42        30.97        22.42         1.78       109.25        25.32 
TCGA-J9-A52E TCGA-KC-A7F6 TCGA-KK-A6DY TCGA-KK-A8IC TCGA-V1-A8WS TCGA-V1-A8WW 
       10.62         8.65       141.21        67.43        15.58        35.44 
TCGA-V1-A9O5 TCGA-VP-A87D TCGA-YL-A9WY 
       63.52        60.92        36.10 

$`9P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
        6.44        29.56        32.45        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       28.37        44.84        41.82        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-5754 TCGA-CH-5761 TCGA-CH-5762 
        1.02        13.02        31.00         2.04         0.92        44.02 
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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       26.99         9.99         2.99        29.00        48.56        57.86 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        56.55        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 
       45.73        46.92        30.31        45.40        64.60        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       62.04        48.53        56.98        60.13        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       62.10        69.63        64.50        68.35        61.87        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       93.70        83.57        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       27.09        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        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87        27.85        30.38        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        15.55        22.36         0.76 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       19.30        27.75        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 
       40.04        33.01        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CL 
       13.55        27.12        13.87         5.85        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       43.66        21.86         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       64.70        86.40        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        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        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       31.79        32.91        63.48        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        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 
       64.04        30.38        22.55         6.64        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       89.49        55.56        66.97        21.80        58.32        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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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        75.75 
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 
       77.79        68.48         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       70.22        24.33        49.91         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       10.13         4.27        11.67        42.81        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 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.78              0.76 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           141.21            165.17 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            35.01             30.51 
[1] "1.8 - 141.2 (35.0)" "0.8 - 165.2 (30.5)"
[1] "hr="     "2.8e+07"
D56V2, continuous
                   vv
clus                 T2  T3  T4
  9P LOSS MUTATED     4  15   2
  9P LOSS WILD-TYPE 183 273   8
D56V3, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T2               4               183
  T3              15               273
  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   7
  9P LOSS WILD-TYPE 330  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     13    7
  9P LOSS WILD-TYPE  330   70
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              13               330
  1               7                70
[1] 2 2
[1] FALSE
D56V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    18   1
  9P LOSS WILD-TYPE 372  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     18    1
  9P LOSS WILD-TYPE  372   58
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               18               372
  YES               1                58
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    21   0
  9P LOSS WILD-TYPE 457  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     21    0
  9P LOSS WILD-TYPE  457   14
                                        clus
vv                                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 21               457
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    13   7   0   0
  9P LOSS WILD-TYPE 300 137   5  15
D56V7, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              13               300
  R1               7               137
  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"
D56V8, continuous
D56V9, continuous
D56V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       0                         0     6
  9P LOSS WILD-TYPE     2                         7   140
D56V11, 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    11   0
  9Q LOSS WILD-TYPE 472   9
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               481 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                0                 9 
$`9Q LOSS MUTATED`
TCGA-4L-AA1F TCGA-EJ-5514 TCGA-EJ-7781 TCGA-FC-7961 TCGA-G9-7521 TCGA-HI-7168 
       11.51        60.13        35.28        15.42        30.97       109.25 
TCGA-J9-A52E TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A9O5 TCGA-YL-A9WY 
       10.62        15.58        35.44        63.52        36.10 

$`9Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 
        3.68        28.37        44.84        41.82        20.22         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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
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-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
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        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        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        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        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-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        35.44        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        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 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       27.75        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CL 
       13.55        27.12        13.87         5.85        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
       21.96        65.82        31.79        32.91        63.48        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 
       67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WV 
       14.73        39.29        61.68        64.04        30.38        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         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        75.75        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        77.79        68.48 
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        70.22        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-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        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 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            10.62              0.76 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           109.25            165.17 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            35.28             30.51 
[1] "10.6 - 109.2 (35.3)" "0.8 - 165.2 (30.5)" 
[1] "hr="     "9200000"
D57V2, continuous
                   vv
clus                 T2  T3  T4
  9Q LOSS MUTATED     2   8   1
  9Q LOSS WILD-TYPE 185 280   9
D57V3, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T2               2               185
  T3               8               280
  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   4
  9Q LOSS WILD-TYPE 337  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6    4
  9Q LOSS WILD-TYPE  337   73
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               6               337
  1               4                73
[1] 2 2
[1] FALSE
D57V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    10   1
  9Q LOSS WILD-TYPE 380  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     10    1
  9Q LOSS WILD-TYPE  380   58
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               10               380
  YES               1                58
[1] 2 2
[1] FALSE
D57V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    11   0
  9Q LOSS WILD-TYPE 467  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     11    0
  9Q LOSS WILD-TYPE  467   14
                                        clus
vv                                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 11               467
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED     6   4   0   0
  9Q LOSS WILD-TYPE 307 140   5  15
D57V7, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0               6               307
  R1               4               140
  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"
D57V8, continuous
D57V9, continuous
D57V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       0                         0     4
  9Q LOSS WILD-TYPE     2                         7   142
D57V11, 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    40   1
  10P LOSS WILD-TYPE 443   8
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                41                451 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                  8 
$`10P LOSS MUTATED`
TCGA-CH-5790 TCGA-KK-A7B4 TCGA-XK-AAJ3 TCGA-2A-A8VT TCGA-CH-5751 TCGA-CH-5788 
       32.02        32.45        41.49        45.14        35.01        26.99 
TCGA-EJ-5518 TCGA-EJ-7784 TCGA-FC-7961 TCGA-G9-6363 TCGA-G9-6377 TCGA-G9-7521 
       69.63        25.68        15.42        45.30        31.50        30.97 
TCGA-HC-7213 TCGA-HC-7232 TCGA-HC-A48F TCGA-HI-7168 TCGA-HI-7171 TCGA-J9-A52B 
       40.08        38.17        22.36       109.25        43.69        13.87 
TCGA-J9-A8CP TCGA-KK-A59Z TCGA-KK-A6E6 TCGA-KK-A8I5 TCGA-M7-A721 TCGA-V1-A8WW 
       12.69        86.40       113.33       101.79        13.15        35.44 
TCGA-V1-A9O5 TCGA-V1-A9Z7 TCGA-VP-A875 TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       63.52        28.73        75.91        58.32        42.94        44.88 
TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YL-A8HL TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SQ 
       37.25        47.15        51.45        45.86        32.45        68.48 
TCGA-YL-A9WK TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L9 TCGA-ZG-A9LS 
       70.22         4.27        11.67        20.28        16.96 

$`10P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-5542 
        1.02        12.00         1.02        15.98        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
       29.56         2.73        41.00        32.19        20.42        55.92 
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        45.30         3.68        28.37        44.84        41.82 
TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 
       20.22        11.51         2.99         6.97        22.06         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       12.99        13.97         1.97        24.03         1.02        13.02 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 
       15.06        24.03         2.04        13.02         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 
       56.98        60.13        60.23        62.10        62.10        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         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-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.31         4.77        28.41        28.83        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       25.94        20.25        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        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       26.66        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-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.44        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       32.91        30.87        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55         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-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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
       18.84        19.30        27.75        88.24        82.92        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK 
       18.18        13.55        27.12         5.85        10.62        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       13.32        15.22        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 
       83.34        64.70       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
       67.59       115.13        68.15        90.74        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        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       34.95        36.13        74.27        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        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        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       16.21        21.14        12.62        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
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        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       37.28        35.08        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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 
       25.18        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 
      119.38       109.58       102.90        23.93        89.49        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       60.92        66.97        21.80        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
        2.99        31.99        31.96        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       36.95        51.81         4.80        25.32        32.61        17.29 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
        4.87        52.96        49.02        48.72        75.75        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-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH 
       53.06        46.29       114.38        77.79         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        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13        42.81        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LU 
       29.85        22.59        19.17        12.43         3.78        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 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              4.27               0.76 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            113.33             165.17 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             38.17              29.56 
[1] "4.3 - 113.3 (38.2)" "0.8 - 165.2 (29.6)"
[1] "hr=" "1.4"
D58V2, continuous
                    vv
clus                  T2  T3  T4
  10P LOSS MUTATED     7  28   6
  10P LOSS WILD-TYPE 180 260   4
D58V3, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T2                7                180
  T3               28                260
  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  16
  10P LOSS WILD-TYPE 321  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     22   16
  10P LOSS WILD-TYPE  321   61
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               22                321
  1               16                 61
[1] 2 2
[1] FALSE
D58V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    33   8
  10P LOSS WILD-TYPE 357  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     33    8
  10P LOSS WILD-TYPE  357   51
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                33                357
  YES                8                 51
[1] 2 2
[1] FALSE
D58V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    40   1
  10P LOSS WILD-TYPE 438  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     40    1
  10P LOSS WILD-TYPE  438   13
                                        clus
vv                                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  40                438
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    19  20   1   0
  10P LOSS WILD-TYPE 294 124   4  15
D58V7, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               19                294
  R1               20                124
  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"
D58V8, continuous
D58V9, continuous
D58V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         0    12
  10P LOSS WILD-TYPE     2                         7   134
D58V11, 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    42   1
  10Q LOSS WILD-TYPE 441   8
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                43                449 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                  8 
$`10Q LOSS MUTATED`
TCGA-CH-5790 TCGA-KK-A7B4 TCGA-2A-A8VT TCGA-CH-5751 TCGA-EJ-5507 TCGA-EJ-5518 
       32.02        32.45        45.14        35.01        47.90        69.63 
TCGA-EJ-7784 TCGA-FC-7961 TCGA-G9-6348 TCGA-G9-6377 TCGA-G9-6499 TCGA-G9-7521 
       25.68        15.42        49.81        31.50        50.73        30.97 
TCGA-HC-7213 TCGA-HC-7232 TCGA-HC-7737 TCGA-HC-8266 TCGA-HC-A48F TCGA-HI-7168 
       40.08        38.17        35.84        15.55        22.36       109.25 
TCGA-HI-7171 TCGA-J9-A52B TCGA-KK-A59Z TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A8I5 
       43.69        13.87        86.40       113.33        90.74       101.79 
TCGA-M7-A721 TCGA-V1-A8WW TCGA-V1-A9O5 TCGA-V1-A9Z7 TCGA-VP-A875 TCGA-VP-A87K 
       13.15        35.44        63.52        28.73        75.91        42.94 
TCGA-VP-AA1N TCGA-XK-AAIV TCGA-XK-AAJT TCGA-XQ-A8TB TCGA-YL-A8HL TCGA-YL-A8SF 
       44.88        37.25        47.15        25.32        51.45        45.14 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A9WK TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L9 
       45.86        32.45        70.22         4.27        11.67        20.28 
TCGA-ZG-A9M4 
       17.98 

$`10Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-5542 
        1.02        12.00         1.02        15.98        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       29.56         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       55.92        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       41.82        20.22        11.51         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-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 
       13.02        31.00         2.04         0.92        44.02        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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
        9.99         2.99        29.00        48.56        57.86        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       46.92        30.31        45.40        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.87        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        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        80.55        68.68 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       40.31        26.66        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-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.44        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7736 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       32.91        30.87        36.26        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       27.75        88.24        82.92        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12         5.85        10.62        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       64.70       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      115.13        68.15        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
       74.27        21.96        65.82        31.79        32.91        63.48 
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        67.46        20.65        62.96        16.21        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-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        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        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.80        58.32        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        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-XQ-A8TA TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
       51.81         4.80        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        48.72        75.75        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO 
       56.52        41.46        28.77        53.06        46.29       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       77.79        68.48         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        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       10.13        42.81        37.94        36.43        29.85        22.59 
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 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              4.27               0.76 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            113.33             165.17 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             38.17              29.23 
[1] "4.3 - 113.3 (38.2)" "0.8 - 165.2 (29.2)"
[1] "hr=" "1.3"
D59V2, continuous
                    vv
clus                  T2  T3  T4
  10Q LOSS MUTATED     9  29   5
  10Q LOSS WILD-TYPE 178 259   5
D59V3, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T2                9                178
  T3               29                259
  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    24  17
  10Q LOSS WILD-TYPE 319  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     24   17
  10Q LOSS WILD-TYPE  319   60
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               24                319
  1               17                 60
[1] 2 2
[1] FALSE
D59V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    35   8
  10Q LOSS WILD-TYPE 355  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     35    8
  10Q LOSS WILD-TYPE  355   51
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                35                355
  YES                8                 51
[1] 2 2
[1] FALSE
D59V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    42   1
  10Q LOSS WILD-TYPE 436  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     42    1
  10Q LOSS WILD-TYPE  436   13
                                        clus
vv                                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  42                436
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    19  23   0   0
  10Q LOSS WILD-TYPE 294 121   5  15
D59V7, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               19                294
  R1               23                121
  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"
D59V8, continuous
D59V9, continuous
D59V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       0                         1    13
  10Q LOSS WILD-TYPE     2                         6   133
D59V11, 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   1
  11P LOSS WILD-TYPE 476   8
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                484 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  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        67.46        28.18        44.88 
TCGA-XQ-A8TA TCGA-ZG-A9KY 
        4.80         4.27 

$`11P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       38.10        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        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        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP 
       13.87         5.85        10.62        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        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        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
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-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM 
       82.36        66.18       113.98        51.25        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 
       30.38        15.58        22.55        35.44         6.64        63.52 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       82.16        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        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        58.32        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 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA 
        2.99        31.99        31.96        37.25        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TB TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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 
       75.75        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        77.79        68.48         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        70.22        24.33        49.91        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       14.53        13.28        10.13        11.67        42.81        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 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              4.27               0.76 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             67.46             165.17 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            26.515             30.760 
[1] "4.3 - 67.5 (26.5)"  "0.8 - 165.2 (30.8)"
[1] "hr=" "11" 
D60V2, continuous
                    vv
clus                  T2  T3  T4
  11P LOSS MUTATED     1   5   1
  11P LOSS WILD-TYPE 186 283   9
D60V3, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T2                1                186
  T3                5                283
  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 339  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    1
  11P LOSS WILD-TYPE  339   76
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                4                339
  1                1                 76
[1] 2 2
[1] FALSE
D60V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     6   1
  11P LOSS WILD-TYPE 384  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    1
  11P LOSS WILD-TYPE  384   58
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 6                384
  YES                1                 58
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     8   0
  11P LOSS WILD-TYPE 470  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8    0
  11P LOSS WILD-TYPE  470   14
                                        clus
vv                                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   8                470
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED     2   5   0   0
  11P LOSS WILD-TYPE 311 139   5  15
D60V7, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                2                311
  R1                5                139
  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"
D60V8, continuous
D60V9, continuous
D60V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       0                         0     0
  11P LOSS WILD-TYPE     2                         7   146
D60V11, multiclass

Clustering(61) Variable = 11Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED     5   0
  11Q LOSS WILD-TYPE 478   9
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                487 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 0                  9 
$`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-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
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        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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 
       28.83        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
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 
       35.44        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CM 
       13.55        27.12        13.87        10.62        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       20.05        47.64        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       61.68        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03 
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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       37.25        40.04        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         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        75.75        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        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       68.48         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
       10.13        11.67        42.81        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 
       13.48 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              4.27               0.76 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             28.18             165.17 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              5.85              30.84 
[1] "4.3 - 28.2 (5.8)"   "0.8 - 165.2 (30.8)"
[1] "hr="     "1200000"
D61V2, continuous
                    vv
clus                  T2  T3  T4
  11Q LOSS MUTATED     0   4   1
  11Q LOSS WILD-TYPE 187 284   9
D61V3, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T2                0                187
  T3                4                284
  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 342  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1    1
  11Q LOSS WILD-TYPE  342   76
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                1                342
  1                1                 76
[1] 2 2
[1] FALSE
D61V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     4   0
  11Q LOSS WILD-TYPE 386  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4    0
  11Q LOSS WILD-TYPE  386   59
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 4                386
  YES                0                 59
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     5   0
  11Q LOSS WILD-TYPE 473  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      5    0
  11Q LOSS WILD-TYPE  473   14
                                        clus
vv                                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   5                473
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED     1   4   0   0
  11Q LOSS WILD-TYPE 312 140   5  15
D61V7, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                1                312
  R1                4                140
  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"
D61V8, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                400 
        TCGA-CH-5753         TCGA-CH-5763         TCGA-CH-5764 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5790         TCGA-CH-5791 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7123         TCGA-EJ-7312 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7325         TCGA-EJ-7791         TCGA-EJ-A46B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A46G         TCGA-EJ-A65J         TCGA-EJ-A6RC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6364         TCGA-HC-7233         TCGA-HC-7748 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7821         TCGA-HC-A76W         TCGA-KC-A7FA 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A7AP         TCGA-KK-A7B3         TCGA-KK-A7B4 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-QU-A6IM         TCGA-XK-AAJ3         TCGA-XK-AAK1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        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-5754         TCGA-CH-5761 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CH-5762         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-5788         TCGA-CH-5789 
"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-7115 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7125         TCGA-EJ-7218         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-7327         TCGA-EJ-7328         TCGA-EJ-7330 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7331         TCGA-EJ-7781         TCGA-EJ-7782 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7783         TCGA-EJ-7784         TCGA-EJ-7785 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7786         TCGA-EJ-7788         TCGA-EJ-7789 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-EJ-7797 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-8468         TCGA-EJ-8469         TCGA-EJ-8470 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-8472         TCGA-EJ-8474         TCGA-EJ-A46D 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A46E         TCGA-EJ-A46F         TCGA-EJ-A65B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A65D         TCGA-EJ-A65E         TCGA-EJ-A65F 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EJ-A65G         TCGA-EJ-A65M         TCGA-EJ-A6RA 
"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-G9-6365         TCGA-G9-6367 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6377 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6379         TCGA-G9-6384         TCGA-G9-6494 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-G9-7510 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-7521         TCGA-G9-7522         TCGA-G9-7523 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G9-7525         TCGA-G9-A9S0         TCGA-G9-A9S7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-H9-A6BY         TCGA-HC-7078         TCGA-HC-7079 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7209         TCGA-HC-7210 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7736         TCGA-HC-7737 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7740         TCGA-HC-7742         TCGA-HC-7744 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-7745         TCGA-HC-7747         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-8216         TCGA-HC-8257         TCGA-HC-8258 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-8260         TCGA-HC-8262         TCGA-HC-8264 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-8265         TCGA-HC-8266         TCGA-HC-A48F 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-A4ZV         TCGA-HC-A631         TCGA-HC-A632 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-A6AL         TCGA-HC-A6AN         TCGA-HC-A6AS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-A6HX         TCGA-HC-A76X         TCGA-HC-A8CY 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-A8D0         TCGA-HC-A8D1         TCGA-HC-A9TE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HC-A9TH         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-A7FD         TCGA-KC-A7FE         TCGA-KK-A59V 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A59X         TCGA-KK-A59Y         TCGA-KK-A59Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A6DY         TCGA-KK-A6E0         TCGA-KK-A6E1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A6E2         TCGA-KK-A6E3         TCGA-KK-A6E4 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A6E5         TCGA-KK-A6E6         TCGA-KK-A6E7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A6E8         TCGA-KK-A7AQ         TCGA-KK-A7AU 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A7AV         TCGA-KK-A7AW         TCGA-KK-A7AY 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A7AZ         TCGA-KK-A7B0         TCGA-KK-A7B1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A7B2         TCGA-KK-A8I4         TCGA-KK-A8I6 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A8I7         TCGA-KK-A8IA         TCGA-KK-A8ID 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KK-A8IJ         TCGA-KK-A8IL         TCGA-M7-A71Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-M7-A722         TCGA-M7-A723         TCGA-M7-A724 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-M7-A725         TCGA-QU-A6IL         TCGA-QU-A6IN 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-QU-A6IO         TCGA-QU-A6IP         TCGA-SU-A7E7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-TP-A8TT         TCGA-TP-A8TV         TCGA-V1-A8MF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A8MJ         TCGA-V1-A8ML         TCGA-V1-A8MM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A8MU         TCGA-V1-A8WL         TCGA-V1-A8WV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A8WW         TCGA-V1-A8X3         TCGA-V1-A9O5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A9O7         TCGA-V1-A9O9         TCGA-V1-A9OA 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A9OL         TCGA-V1-A9OX         TCGA-V1-A9OY 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A9Z7         TCGA-V1-A9Z8         TCGA-V1-A9Z9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-V1-A9ZG         TCGA-V1-A9ZI         TCGA-V1-A9ZK 
"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-AAJA         TCGA-XK-AAJP         TCGA-XK-AAJR 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-XK-AAJT         TCGA-XK-AAJU         TCGA-XQ-A8TB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-Y6-A8TL         TCGA-Y6-A9XI         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-A9L1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9L2         TCGA-ZG-A9L4         TCGA-ZG-A9L5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9L6         TCGA-ZG-A9L9         TCGA-ZG-A9LB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9LM         TCGA-ZG-A9LN         TCGA-ZG-A9LS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9LU         TCGA-ZG-A9LY         TCGA-ZG-A9LZ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9M4         TCGA-ZG-A9MC         TCGA-ZG-A9N3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ZG-A9ND 
"11Q LOSS WILD-TYPE" 
D61V9, continuous
D61V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       0                         0     0
  11Q LOSS WILD-TYPE     2                         7   146
D61V11, multiclass

Clustering(62) Variable = 12P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    47   0
  12P LOSS WILD-TYPE 436   9
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                47                445 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                  9 
$`12P LOSS MUTATED`
TCGA-G9-6364 TCGA-KC-A7FA TCGA-2A-A8VT TCGA-CH-5744 TCGA-CH-5751 TCGA-CH-5766 
       39.39        19.66        45.14         1.97        35.01         1.02 
TCGA-EJ-5510 TCGA-EJ-5514 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-7781 
       62.04        60.13        64.50        68.35        62.76        35.28 
TCGA-EJ-7784 TCGA-EJ-8472 TCGA-EJ-A7NH TCGA-EJ-A8FS TCGA-G9-6379 TCGA-G9-7521 
       25.68        24.85        15.58         8.75        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       109.25        30.94        13.87 
TCGA-KC-A4BV TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A7AZ TCGA-KK-A8I4 TCGA-KK-A8IA 
       43.66        72.26       113.33        49.94        74.27        63.48 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-V1-A8MF TCGA-V1-A8WV TCGA-V1-A8WW TCGA-VP-A87J 
       18.84         5.69        47.64        22.55        35.44        58.32 
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        70.22        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-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       21.96        14.83        28.70        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP TCGA-KK-A7B3 
        3.48         7.00        32.61        40.67         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       55.92        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       41.82        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-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5767 
       31.00         2.04         0.92        44.02        23.01        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 
       45.40        47.90        64.60        48.13        48.53        56.98 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5524 
       60.23        62.10        62.10        69.63        74.93        61.87 
TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       36.66        58.45        60.23        41.85        60.10        88.34 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       93.70        83.57        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       27.09        30.35        27.68         6.28        24.39        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.87        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
       11.61         8.22        14.20         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
       10.82         9.27         9.83         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        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        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        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        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-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.44        28.18        32.68        26.01        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       30.38        22.55        17.95         1.58        15.88        15.55 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        0.76         1.78         2.01         1.61        17.42         2.33 
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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       18.84        19.30        27.75        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        40.04        33.01        25.32        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK 
       18.18        13.55        27.12         5.85        10.62        10.55 
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-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 
       83.34        64.70        86.40       141.21        48.76       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
       67.59       115.13        68.15        90.74        58.19        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B1 
       58.36        27.02        34.65        57.67        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       36.13       101.79        21.96        65.82        31.79        32.91 
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        67.46        20.65        62.96        16.21        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL 
       12.62        13.15        34.85        25.08        29.23         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       20.05        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 
       61.68        64.04        30.38        15.58         6.64        63.52 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       82.16        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       21.80        42.94        14.76        32.19        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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        75.75 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH 
       62.14        60.56        16.83        56.52        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        77.79        68.48 
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 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        42.81        37.94        36.43        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9ND 
       19.17         3.78        12.16        22.75        14.96        13.48 
TCGA-ZG-A9NI 
        4.34 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1.02               0.76 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            113.33             165.17 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             35.28              30.38 
[1] "1.0 - 113.3 (35.3)" "0.8 - 165.2 (30.4)"
[1] "hr="     "7.9e+07"
D62V2, continuous
                    vv
clus                  T2  T3  T4
  12P LOSS MUTATED    10  34   3
  12P LOSS WILD-TYPE 177 254   7
D62V3, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T2               10                177
  T3               34                254
  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    29  18
  12P LOSS WILD-TYPE 314  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     29   18
  12P LOSS WILD-TYPE  314   59
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               29                314
  1               18                 59
[1] 2 2
[1] FALSE
D62V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    36   7
  12P LOSS WILD-TYPE 354  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     36    7
  12P LOSS WILD-TYPE  354   52
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                36                354
  YES                7                 52
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    47   0
  12P LOSS WILD-TYPE 431  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     47    0
  12P LOSS WILD-TYPE  431   14
                                        clus
vv                                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  47                431
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    28  15   1   3
  12P LOSS WILD-TYPE 285 129   4  12
D62V7, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               28                285
  R1               15                129
  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"
D62V8, continuous
D62V9, continuous
D62V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0    12
  12P LOSS WILD-TYPE     2                         7   134
D62V11, 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    20   0
  12Q LOSS WILD-TYPE 463   9
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                472 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 0                  9 
$`12Q LOSS MUTATED`
TCGA-KC-A7FA TCGA-CH-5751 TCGA-EJ-5510 TCGA-EJ-5514 TCGA-EJ-5526 TCGA-EJ-7781 
       19.66        35.01        62.04        60.13        62.76        35.28 
TCGA-EJ-7784 TCGA-G9-7521 TCGA-HC-8216 TCGA-HI-7168 TCGA-J9-A52B TCGA-KC-A4BV 
       25.68        30.97        22.42       109.25        13.87        43.66 
TCGA-KK-A6E1 TCGA-KK-A7AZ TCGA-KK-A8IA TCGA-MG-AAMC TCGA-V1-A8WV TCGA-V1-A8WW 
       72.26        49.94        63.48         5.69        22.55        35.44 
TCGA-VP-AA1N TCGA-ZG-A9M4 
       44.88        17.98 

$`12Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP 
       31.43         3.48         7.00        32.61        40.67         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       64.60        48.13        48.53        56.98        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        69.63        64.50        74.93        68.35        61.87 
TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       36.66        58.45        60.23        41.85        60.10        88.34 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       93.70        83.57        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       27.09        30.35        27.68         6.28        24.39        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.87        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        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-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87        27.85        30.38        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        15.55        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-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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       18.84        19.30        27.75        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        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E 
       17.85        18.18        13.55        27.12         5.85        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        15.22        12.69        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-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        83.34        64.70        86.40       141.21        48.76 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       65.82        31.79        32.91        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        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08        29.23        18.84         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       64.04        30.38        15.58         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58       102.90 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        89.49        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 
       58.32        42.94        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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 
       75.75        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        77.79        68.48         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        70.22        24.33        49.91        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       14.53        13.28        10.13         4.27        11.67        42.81 
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-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              5.69               0.76 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            109.25             165.17 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             35.36              30.38 
[1] "5.7 - 109.2 (35.4)" "0.8 - 165.2 (30.4)"
[1] "hr="     "2.6e+07"
D63V2, continuous
                    vv
clus                  T2  T3  T4
  12Q LOSS MUTATED     4  15   1
  12Q LOSS WILD-TYPE 183 273   9
D63V3, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T2                4                183
  T3               15                273
  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   8
  12Q LOSS WILD-TYPE 331  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     12    8
  12Q LOSS WILD-TYPE  331   69
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               12                331
  1                8                 69
[1] 2 2
[1] FALSE
D63V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    17   2
  12Q LOSS WILD-TYPE 373  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     17    2
  12Q LOSS WILD-TYPE  373   57
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                17                373
  YES                2                 57
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    20   0
  12Q LOSS WILD-TYPE 458  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     20    0
  12Q LOSS WILD-TYPE  458   14
                                        clus
vv                                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  20                458
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    14   4   0   2
  12Q LOSS WILD-TYPE 299 140   5  13
D63V7, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               14                299
  R1                4                140
  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"
D63V8, continuous
D63V9, continuous
D63V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0     7
  12Q LOSS WILD-TYPE     2                         7   139
D63V11, 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    77   1
  13Q LOSS WILD-TYPE 406   8
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                78                414 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                  8 
$`13Q LOSS MUTATED`
TCGA-KK-A7B4 TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5751 TCGA-CH-5771 TCGA-CH-5788 
       32.45        11.51         2.99        35.01        13.02        26.99 
TCGA-EJ-5495 TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5516 
       57.86        46.92        47.90        48.53        60.13        62.10 
TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7781 TCGA-EJ-7783 
       74.93        36.66        25.35        33.83        35.28        25.87 
TCGA-EJ-7786 TCGA-EJ-8472 TCGA-EJ-A46D TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-FC-7961 
       36.03        24.85        20.58         8.22        15.58        15.42 
TCGA-G9-6329 TCGA-G9-6378 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-HC-7213 
       41.62        37.97        38.96        27.91        30.97        40.08 
TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AS TCGA-HI-7168 
       15.55         0.76         2.01         1.61         1.45       109.25 
TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       13.87        10.62        72.26       113.33        90.74        58.19 
TCGA-KK-A8IA TCGA-KK-A8IG TCGA-KK-A8IH TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A9O5 
       63.48        82.36        66.18        22.55        35.44        63.52 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OL TCGA-VP-A875 TCGA-VP-A876 
       82.16        94.36        20.91        62.89        75.91       109.58 
TCGA-VP-A87D TCGA-XJ-A9DI TCGA-XK-AAIV TCGA-XQ-A8TA TCGA-YJ-A8SW TCGA-YL-A8S9 
       60.92        48.03        37.25         4.80         4.87        60.56 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       56.52        41.46        45.14        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A9WK TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 
      114.38        68.48        70.22         4.27        37.94        36.43 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9NI 
       20.28        19.17        12.43        19.04        22.75         4.34 

$`13Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
        6.44        29.56         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5738 TCGA-CH-5739 
       28.37        44.84        41.82        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-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 
       13.02        31.00         2.04         0.92        44.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5789 TCGA-CH-5792 
        1.02        15.06        24.03         2.04         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       29.00        48.56        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       44.88        38.50        45.73        30.31        45.40        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 
       48.13        62.04        56.98        60.23        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       64.50        68.35        61.87        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       33.14        27.09        30.35        27.68         6.28        24.39 
TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       38.37        25.68        38.70        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8474 TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       25.18        17.23        25.74        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
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-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 
       28.83        22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6379 
       39.95        38.01        40.31        26.66        31.50        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-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       52.93        35.44        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       28.60        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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-A6HX 
       22.36         1.78         2.20        17.42         2.33         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       27.75        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       13.55        27.12         5.85        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       64.70        86.40       141.21        48.76       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
      115.13        68.15        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-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
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-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       69.27        26.43       113.98        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9OF 
       61.68        64.04        30.38        15.58         6.64        38.93 
TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       79.00        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A878 
       41.42        44.91        25.78        16.31       119.38       102.90 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       23.93        89.49        55.56        66.97        21.80        58.32 
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        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       37.05        48.03        42.08         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-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        25.32        32.61        17.29        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SH 
       51.45        48.72        75.75        62.14        16.83        28.77 
TCGA-YL-A8SI TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       53.06        77.79         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        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LN 
       10.13        11.67        42.81        29.85        22.59         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       16.96        12.16        17.98        14.96        11.47        13.48 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.76               0.89 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            114.38             165.17 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            36.545             29.395 
[1] "0.8 - 114.4 (36.5)" "0.9 - 165.2 (29.4)"
[1] "hr=" "1.5"
D64V2, continuous
                    vv
clus                  T2  T3  T4
  13Q LOSS MUTATED    16  58   3
  13Q LOSS WILD-TYPE 171 230   7
D64V3, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T2               16                171
  T3               58                230
  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    51  21
  13Q LOSS WILD-TYPE 292  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     51   21
  13Q LOSS WILD-TYPE  292   56
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               51                292
  1               21                 56
[1] 2 2
[1] FALSE
D64V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    61  11
  13Q LOSS WILD-TYPE 329  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     61   11
  13Q LOSS WILD-TYPE  329   48
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                61                329
  YES               11                 48
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    77   1
  13Q LOSS WILD-TYPE 401  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     77    1
  13Q LOSS WILD-TYPE  401   13
                                        clus
vv                                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  77                401
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    39  33   0   3
  13Q LOSS WILD-TYPE 274 111   5  12
D64V7, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               39                274
  R1               33                111
  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"
D64V8, continuous
D64V9, continuous
D64V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         2    19
  13Q LOSS WILD-TYPE     2                         5   127
D64V11, 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 459   8
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                467 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                  8 
$`14Q LOSS MUTATED`
TCGA-HC-7821 TCGA-HC-A76W TCGA-EJ-7783 TCGA-EJ-7784 TCGA-G9-6361 TCGA-G9-6499 
       31.43         7.00        25.87        25.68        46.52        50.73 
TCGA-G9-7521 TCGA-G9-7523 TCGA-HC-7213 TCGA-HI-7171 TCGA-J4-A67O TCGA-KK-A8IA 
       30.97        28.18        40.08        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        75.75        56.52        45.86        32.45 
TCGA-YL-A8SQ TCGA-YL-A9WX TCGA-ZG-A9KY TCGA-ZG-A9L5 TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       68.48        49.91         4.27        29.85        22.75        17.98 
TCGA-ZG-A9N3 
       11.47 

$`14Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-A6AQ TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 
        3.48        32.61        40.67        19.66         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7785 TCGA-EJ-7786 
        6.28        24.39        35.28        38.37        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       28.24        36.33        45.90         3.75        42.94        32.32 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       77.16        76.41        38.10        24.85        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         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        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        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        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       50.70        67.92        47.15        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        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-G9-7522 
       56.75        64.18        52.93        38.96        27.91        35.44 
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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        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        15.55        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-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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        88.24        82.92 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        40.04        33.01        25.32        30.94        30.81 
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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       18.18        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        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-A7FD 
       19.96        44.35        43.66        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        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        32.91 
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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        41.46        45.14        28.77        53.06 
TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       46.29       114.38        77.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       60.99        70.22        24.33        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13        11.67        42.81        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-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       19.04        12.16        14.96        13.48         4.34 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              4.27               0.76 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             75.91             165.17 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             32.45              30.38 
[1] "4.3 - 75.9 (32.5)"  "0.8 - 165.2 (30.4)"
[1] "hr=" "2.6"
D65V2, continuous
                    vv
clus                  T2  T3  T4
  14Q LOSS MUTATED     2  21   2
  14Q LOSS WILD-TYPE 185 267   8
D65V3, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T2                2                185
  T3               21                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"
D65V4, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    16   9
  14Q LOSS WILD-TYPE 327  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     16    9
  14Q LOSS WILD-TYPE  327   68
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               16                327
  1                9                 68
[1] 2 2
[1] FALSE
D65V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    21   3
  14Q LOSS WILD-TYPE 369  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     21    3
  14Q LOSS WILD-TYPE  369   56
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                21                369
  YES                3                 56
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    24   1
  14Q LOSS WILD-TYPE 454  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     24    1
  14Q LOSS WILD-TYPE  454   13
                                        clus
vv                                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  24                454
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED     9  14   0   1
  14Q LOSS WILD-TYPE 304 130   5  14
D65V7, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0                9                304
  R1               14                130
  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"
D65V8, continuous
D65V9, continuous
D65V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       0                         0     7
  14Q LOSS WILD-TYPE     2                         7   139
D65V11, 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    34   1
  15Q LOSS WILD-TYPE 449   8
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                35                457 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                  8 
$`15Q LOSS MUTATED`
TCGA-CH-5753 TCGA-HC-7821 TCGA-KC-A7FA TCGA-CH-5751 TCGA-EJ-5507 TCGA-EJ-7783 
        1.02        31.43        19.66        35.01        47.90        25.87 
TCGA-FC-A4JI TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-7749 TCGA-HC-8216 TCGA-HI-7168 
       28.83        30.97        40.08        23.80        22.42       109.25 
TCGA-HI-7171 TCGA-J9-A52E TCGA-J9-A8CL TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A8IA 
       43.69        10.62        13.32        86.40        48.76        63.48 
TCGA-V1-A8WS TCGA-V1-A9O7 TCGA-V1-A9OL TCGA-VP-A872 TCGA-XK-AAJA TCGA-XK-AAJT 
       15.58        82.16        62.89       119.38        30.58        47.15 
TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SQ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 
       75.75        56.52        68.48         4.27        11.67        29.85 
TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       20.28        12.43        22.75        17.98        11.47 

$`15Q LOSS WILD-TYPE`
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
       12.00         1.02        15.98        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-A6AQ 
       14.83        28.70        39.39        44.55        26.04         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 
        7.00        32.61        40.67         6.44        29.56        32.45 
TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
        2.73        41.00        41.49        32.19        20.42        55.92 
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       45.14        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       41.82        20.22        11.51         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-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 
       13.02        31.00         2.04         0.92        44.02        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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
        9.99         2.99        29.00        48.56        57.86        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       46.92        30.31        45.40        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        64.50        74.93        68.35        61.87        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       93.70        83.57        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       27.09        30.35        27.68         6.28        24.39        35.28 
TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       17.46        23.70        24.59        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 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       27.75        88.24        82.92        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP 
       27.12        13.87         5.85        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
      141.21        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        32.91 
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        67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55        35.44         6.64        63.52        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       38.93        79.00        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        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-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       40.04        41.39        36.95        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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-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 
       77.79         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LB 
       10.13        42.81        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               0.76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            119.38             165.17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             30.58              30.71 
[1] "1.0 - 119.4 (30.6)" "0.8 - 165.2 (30.7)"
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                  T2  T3  T4
  15Q LOSS MUTATED     1  31   3
  15Q LOSS WILD-TYPE 186 257   7
D66V3, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T2                1                186
  T3               31                257
  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    19  13
  15Q LOSS WILD-TYPE 324  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19   13
  15Q LOSS WILD-TYPE  324   64
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               19                324
  1               13                 64
[1] 2 2
[1] FALSE
D66V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    26   7
  15Q LOSS WILD-TYPE 364  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     26    7
  15Q LOSS WILD-TYPE  364   52
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                26                364
  YES                7                 52
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    34   1
  15Q LOSS WILD-TYPE 444  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     34    1
  15Q LOSS WILD-TYPE  444   13
                                        clus
vv                                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  34                444
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    17  16   0   1
  15Q LOSS WILD-TYPE 296 128   5  14
D66V7, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               17                296
  R1               16                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"
D66V8, continuous
D66V9, continuous
D66V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         0     9
  15Q LOSS WILD-TYPE     2                         7   137
D66V11, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q 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(67) Variable = 16P LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    31   0
  16P LOSS WILD-TYPE 452   9
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                31                461 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                  9 
$`16P LOSS MUTATED`
TCGA-EJ-7123 TCGA-HC-A76W TCGA-KC-A7FA TCGA-KK-A7AP TCGA-CH-5739 TCGA-EJ-5498 
       84.56         7.00        19.66         6.44        22.06        56.55 
TCGA-EJ-5514 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-8469 TCGA-EJ-A7NH TCGA-G9-6329 
       60.13        35.28        25.68        76.41        15.58        41.62 
TCGA-G9-7523 TCGA-HC-7078 TCGA-HC-7749 TCGA-HC-A4ZV TCGA-HC-A6HX TCGA-HC-A6HY 
       28.18        65.26        23.80         0.76         1.25         4.41 
TCGA-HC-A9TH TCGA-J4-A83I TCGA-J9-A8CK TCGA-J9-A8CL TCGA-KK-A59Z TCGA-KK-A6E7 
       27.75        22.52        10.55        13.32        86.40        90.74 
TCGA-KK-A8IG TCGA-V1-A9OA TCGA-VP-AA1N TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A8SQ 
       82.36        20.91        44.88        75.75        45.86        68.48 
TCGA-ZG-A9LZ 
       22.75 

$`16P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       49.74        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB 
        3.48        32.61        40.67        29.56        32.45         2.73 
TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT 
       41.00        41.49        32.19        20.42        55.92        45.14 
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        45.30         3.68        28.37        44.84        41.82 
TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 
       20.22        11.51         2.99         6.97         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
       13.97         1.97        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        19.56        13.32 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       56.98        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       32.32        77.16        38.10        24.85        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         8.22 
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        28.83        22.36        17.23        25.94        20.25 
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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
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 
       35.44        32.68        26.01        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        69.53        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 
       30.84        17.46        23.70        24.59        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        27.85        30.38        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 
       22.32         1.58        15.88        15.55        22.36         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HI-7168 
        4.93         9.53        25.48        18.84        19.30       109.25 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J 
       27.39         6.02        25.28        27.91        16.83        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       13.87         5.85        10.62        15.22        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-A6DY 
        8.88        11.57       113.10        83.34        64.70       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
      113.33        58.19        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-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
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-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-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       67.46        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       22.55        35.44         6.64        63.52        82.16        94.36 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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 
       25.18        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 
      119.38        75.91       109.58       102.90        23.93        89.49 
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        58.32        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        12.36        37.05        48.03 
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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       37.25        40.04        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         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-A8SR TCGA-YL-A9WH 
       46.29        32.45       114.38        77.79         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        70.22        24.33        49.91        36.10 
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-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        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-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.76               0.89 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             90.74             165.17 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             27.75              30.81 
[1] "0.8 - 90.7 (27.8)"  "0.9 - 165.2 (30.8)"
[1] "hr="     "2.7e+07"
D67V2, continuous
                    vv
clus                  T2  T3  T4
  16P LOSS MUTATED    10  21   0
  16P LOSS WILD-TYPE 177 267  10
D67V3, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T2               10                177
  T3               21                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"
D67V4, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    24   3
  16P LOSS WILD-TYPE 319  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     24    3
  16P LOSS WILD-TYPE  319   74
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               24                319
  1                3                 74
[1] 2 2
[1] FALSE
D67V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    22   3
  16P LOSS WILD-TYPE 368  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     22    3
  16P LOSS WILD-TYPE  368   56
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                22                368
  YES                3                 56
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    31   0
  16P LOSS WILD-TYPE 447  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     31    0
  16P LOSS WILD-TYPE  447   14
                                        clus
vv                                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  31                447
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    17  13   0   1
  16P LOSS WILD-TYPE 296 131   5  14
D67V7, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               17                296
  R1               13                131
  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"
D67V8, continuous
D67V9, continuous
D67V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         0     9
  16P LOSS WILD-TYPE     2                         7   137
D67V11, 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   106   1
  16Q LOSS WILD-TYPE 377   8
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               107                385 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                  8 
$`16Q LOSS MUTATED`
TCGA-CH-5764 TCGA-CH-5791 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-HC-7821 TCGA-HC-A76W 
        1.02        33.01        84.56        36.13        31.43         7.00 
TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B4 TCGA-2A-A8VT TCGA-CH-5739 TCGA-CH-5751 
       19.66         6.44        32.45        45.14        22.06        35.01 
TCGA-CH-5788 TCGA-EJ-5495 TCGA-EJ-5498 TCGA-EJ-5514 TCGA-EJ-5525 TCGA-EJ-5527 
       26.99        57.86        56.55        60.13        36.66        58.45 
TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7789 
       33.83        30.35        35.28        25.87        25.68        36.33 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-A46F TCGA-EJ-A7NH TCGA-EJ-A7NM TCGA-FC-7961 
       76.41        38.10        25.74        15.58         4.21        15.42 
TCGA-FC-A5OB TCGA-G9-6329 TCGA-G9-6343 TCGA-G9-6362 TCGA-G9-6384 TCGA-G9-6496 
       22.36        41.62        80.55        47.44        25.15        56.75 
TCGA-G9-7521 TCGA-G9-7523 TCGA-HC-7078 TCGA-HC-7213 TCGA-HC-7736 TCGA-HC-7742 
       30.97        28.18        65.26        40.08        36.26        30.84 
TCGA-HC-7749 TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6HX 
       23.80        22.42        22.36         0.76         2.01         1.25 
TCGA-HC-A6HY TCGA-HC-A8D0 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7171 
        4.41        25.48        19.30        27.75       109.25        43.69 
TCGA-J4-A83I TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CP TCGA-KC-A4BV 
       22.52        13.87        10.55        13.32        12.69        43.66 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AU TCGA-KK-A8I6 
       86.40       141.21       113.33        90.74        58.36        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IK TCGA-QU-A6IO 
       65.82        31.79        26.43        82.36        67.46       122.17 
TCGA-TK-A8OK TCGA-V1-A8MG TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
        0.89        28.18        22.55         6.64        63.52        82.16 
TCGA-V1-A9OA TCGA-V1-A9ZI TCGA-VN-A88M TCGA-VN-A88Q TCGA-VP-A87K TCGA-VP-AA1N 
       20.91        53.92         6.21        44.91        42.94        44.88 
TCGA-X4-A8KQ TCGA-XJ-A83H TCGA-XK-AAIR TCGA-XK-AAJP TCGA-XK-AAJR TCGA-YL-A8HM 
       45.47        42.08        31.96        41.39        36.95        48.72 
TCGA-YL-A8HO TCGA-YL-A8SC TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A8SR 
       75.75        41.46        45.86        32.45        68.48         8.98 
TCGA-YL-A9WK TCGA-YL-A9WX TCGA-ZG-A9L1 TCGA-ZG-A9L4 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       70.22        49.91        42.81        36.43        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       12.43        22.75        17.98        14.96        11.47 

$`16Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5772 TCGA-CH-5790 TCGA-EJ-5542 TCGA-EJ-7325 
        1.02        12.00        15.98        32.02        49.74        35.18 
TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 
       36.76        21.60        21.96        14.83        28.70        39.39 
TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-A6AQ TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7B3 
       44.55        26.04         3.48        32.61        40.67        29.56 
TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
        2.73        41.00        41.49        32.19        20.42        55.92 
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        45.30         3.68        28.37        44.84        41.82 
TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 
       20.22        11.51         2.99         6.97         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-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
       24.03         2.04        13.02         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       48.56        19.56        13.32        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        46.92        30.31        45.40        47.90        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        62.04        48.53        56.98        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        69.63        64.50        74.93        68.35        61.87 
TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       62.76        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7321 TCGA-EJ-7328 
       83.57        37.81        33.14        25.35        27.09        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
        6.28        24.39        38.37        38.70        36.03        28.24 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8472 
       45.90         3.75        42.94        32.32        77.16        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       25.18        20.58        17.23        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A8FN TCGA-EJ-A8FO 
        8.22        14.20         6.48        15.65        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-A4JI TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 
       28.83        17.23        25.94        20.25        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6347 TCGA-G9-6348 
       67.99        66.67        83.87        55.76        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 
       67.33        50.70        67.92        47.15        46.52        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6494 
       26.66        31.50        37.97        58.45        27.29        58.22 
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        35.44 
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-7077 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        69.53        38.93        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        40.14        28.60        32.91        30.87        38.17 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       35.84        31.69        23.57        17.46        23.70        24.59 
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-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        28.27        23.87        27.85        30.38        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A631 
       17.95        22.32         1.58        15.88        15.55         1.78 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A76X 
        2.20         1.61        17.42         2.33         1.45         4.93 
TCGA-HC-A8CY TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 
        9.53        18.84        88.24        82.92        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-KC-A4BL TCGA-KC-A4BN 
       27.12         5.85        10.62        15.22        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        83.34        64.70        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AV 
       67.59       115.13        68.15        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       74.27       101.79        32.91        63.48        67.43        69.27 
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        62.96        16.21 
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-A6IN TCGA-QU-A6IP TCGA-SU-A7E7 
       18.84         5.69         3.19       140.19        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       17.29        20.05        47.64        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WW 
       39.29        61.68        64.04        30.38        15.58        35.44 
TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       94.36        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N 
       45.47        44.75         8.84        25.51        24.53        25.18 
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       119.38        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        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        58.32        14.76        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       37.05        48.03        48.03         9.04         2.99        31.99 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       37.25        40.04        30.58        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       51.45        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        77.79        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        36.10         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 
              0.76               0.92 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            141.21             165.17 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             32.45              29.85 
[1] "0.8 - 141.2 (32.5)" "0.9 - 165.2 (29.9)"
[1] "hr=" "2.6"
D68V2, continuous
                    vv
clus                  T2  T3  T4
  16Q LOSS MUTATED    25  78   3
  16Q LOSS WILD-TYPE 162 210   7
D68V3, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T2               25                162
  T3               78                210
  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    73  24
  16Q LOSS WILD-TYPE 270  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     73   24
  16Q LOSS WILD-TYPE  270   53
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               73                270
  1               24                 53
[1] 2 2
[1] FALSE
D68V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    83  15
  16Q LOSS WILD-TYPE 307  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     83   15
  16Q LOSS WILD-TYPE  307   44
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                83                307
  YES               15                 44
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   104   3
  16Q LOSS WILD-TYPE 374  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    104    3
  16Q LOSS WILD-TYPE  374   11
                                        clus
vv                                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 104                374
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                3                 11
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    57  44   0   2
  16Q LOSS WILD-TYPE 256 100   5  13
D68V7, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               57                256
  R1               44                100
  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"
D68V8, continuous
D68V9, continuous
D68V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         1    29
  16Q LOSS WILD-TYPE     2                         6   117
D68V11, 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    74   2
  17P LOSS WILD-TYPE 409   7
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                76                416 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                  7 
$`17P LOSS MUTATED`
TCGA-CH-5764 TCGA-CH-5790 TCGA-KK-A7AP TCGA-KK-A7B4 TCGA-4L-AA1F TCGA-CH-5754 
        1.02        32.02         6.44        32.45        11.51         2.04 
TCGA-CH-5761 TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5526 
        0.92        47.90        60.13        64.50        74.93        62.76 
TCGA-EJ-7315 TCGA-EJ-7781 TCGA-EJ-7797 TCGA-EJ-A46F TCGA-EJ-A7NH TCGA-FC-A4JI 
       33.14        35.28        32.32        25.74        15.58        28.83 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       26.66        31.50        58.22        50.73        52.93        38.96 
TCGA-G9-7521 TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7742 
       30.97        23.93        65.26        40.08        32.91        30.84 
TCGA-HC-7744 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A9TE TCGA-HI-7168 
       17.46        15.55        22.36         0.76        19.30       109.25 
TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E4 
       13.87        10.62        86.40       141.21        72.26       115.13 
TCGA-KK-A6E6 TCGA-KK-A8I6 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8IG TCGA-KK-A8IK 
      113.33        21.96        63.48        67.43        82.36        67.46 
TCGA-M7-A725 TCGA-V1-A8ML TCGA-V1-A8WS TCGA-V1-A9Z7 TCGA-VP-A875 TCGA-VP-A87C 
       18.84        14.73        15.58        28.73        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87K TCGA-VP-AA1N TCGA-XK-AAJA TCGA-XQ-A8TA TCGA-Y6-A9XI 
       60.92        42.94        44.88        30.58         4.80        17.29 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SK TCGA-YL-A8SL 
       49.02        51.45        75.75        56.52        46.29        32.45 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-ZG-A9L0 TCGA-ZG-A9L4 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       68.48        14.04        11.67        36.43        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       12.43        19.04        17.98        11.47 

$`17P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-5542 TCGA-EJ-7123 
        1.02        12.00        15.98        33.01        49.74        84.56 
TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J 
       36.13        35.18        36.76        21.60        21.96        14.83 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ 
       28.70        39.39        44.55        26.04        31.43         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7B3 TCGA-KK-A8IB 
        7.00        32.61        40.67        19.66        29.56         2.73 
TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT 
       41.00        41.49        32.19        20.42        55.92        45.14 
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        45.30         3.68        28.37        44.84        41.82 
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-5751 
       13.97         1.97        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       31.00        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 
       64.60        48.13        62.04        48.53        56.98        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       62.10        62.10        69.63        68.35        61.87        36.66 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       83.57        37.81        25.35        33.83        27.09        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-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       42.94        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       20.58        17.23        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         8.22 
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-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       15.42        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
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-G9-6496 TCGA-G9-6498 TCGA-G9-7519 TCGA-G9-7522 
       25.15        27.29        56.75        64.18        27.91        35.44 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       28.18        32.68        26.01         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        69.53        38.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.54        40.14        28.60        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       35.84        31.69        23.57        23.70        24.59        23.80 
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        27.85        30.38 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A631 
       22.55        17.95        22.32         1.58        15.88         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       27.75        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        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-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       13.55        27.12         5.85        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 
       64.70        48.76       165.17        67.59        68.15        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH 
       65.82        31.79        32.91        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        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8WW 
       39.29        61.68        64.04        30.38        22.55        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
      102.90        23.93        89.49        66.97        21.80        58.32 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19        12.36        37.05        48.03 
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-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       37.25        40.04        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HM TCGA-YL-A8S8 
       25.32        32.61         4.87        52.96        48.72        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-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ 
       45.86       114.38        77.79         8.98        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L5 
       13.28        10.13         4.27        42.81        37.94        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC 
       22.59         3.78        16.96        12.16        22.75        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.76               0.89 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            141.21             165.17 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            32.385             30.115 
[1] "0.8 - 141.2 (32.4)" "0.9 - 165.2 (30.1)"
[1] "hr=" "1.2"
D69V2, continuous
                    vv
clus                  T2  T3  T4
  17P LOSS MUTATED    15  58   1
  17P LOSS WILD-TYPE 172 230   9
D69V3, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T2               15                172
  T3               58                230
  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    50  21
  17P LOSS WILD-TYPE 293  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     50   21
  17P LOSS WILD-TYPE  293   56
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               50                293
  1               21                 56
[1] 2 2
[1] FALSE
D69V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    58  13
  17P LOSS WILD-TYPE 332  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     58   13
  17P LOSS WILD-TYPE  332   46
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                58                332
  YES               13                 46
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    75   1
  17P LOSS WILD-TYPE 403  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     75    1
  17P LOSS WILD-TYPE  403   13
                                        clus
vv                                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  75                403
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED    40  33   0   2
  17P LOSS WILD-TYPE 273 111   5  13
D69V7, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               40                273
  R1               33                111
  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"
D69V8, continuous
D69V9, continuous
D69V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         0    22
  17P LOSS WILD-TYPE     2                         7   124
D69V11, 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   2
  17Q LOSS WILD-TYPE 465   7
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                20                472 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                  7 
$`17Q LOSS MUTATED`
TCGA-KK-A7AP TCGA-G9-6499 TCGA-HC-7213 TCGA-HC-7744 TCGA-HC-A48F TCGA-J9-A52E 
        6.44        50.73        40.08        17.46        22.36        10.62 
TCGA-KK-A6E4 TCGA-KK-A8IA TCGA-KK-A8IG TCGA-M7-A725 TCGA-V1-A9OL TCGA-VP-A875 
      115.13        63.48        82.36        18.84        62.89        75.91 
TCGA-VP-AA1N TCGA-XK-AAJA TCGA-XQ-A8TA TCGA-YL-A8HO TCGA-YL-A8SQ TCGA-ZG-A9L4 
       44.88        30.58         4.80        75.75        68.48        36.43 
TCGA-ZG-A9LM TCGA-ZG-A9M4 
       12.43        17.98 

$`17Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        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        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        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-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        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        64.01        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-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        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        27.85        30.38        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        15.55         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK 
       18.18        13.55        27.12        13.87         5.85        10.55 
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        83.34        64.70        86.40       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
       72.26       165.17        67.59        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID 
       21.96        65.82        31.79        32.91        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        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08        29.23         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 
       64.04        30.38        15.58        22.55        35.44         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         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        25.18        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       119.38       109.58       102.90 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        89.49        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 
       58.32        42.94        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJP TCGA-XK-AAJR 
       31.99        31.96        37.25        40.04        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       47.15        51.81        25.32        32.61        17.29         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-A8SR 
       45.86        46.29        32.45       114.38        77.79         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        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        42.81        37.94        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       19.17         3.78        16.96        19.04        12.16        22.75 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              4.80               0.76 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            115.13             165.17 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            38.255             30.445 
[1] "4.8 - 115.1 (38.3)" "0.8 - 165.2 (30.4)"
[1] "hr=" "3.9"
D70V2, continuous
                    vv
clus                  T2  T3  T4
  17Q LOSS MUTATED     2  17   0
  17Q LOSS WILD-TYPE 185 271  10
D70V3, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T2                2                185
  T3               17                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"
D70V4, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    14   5
  17Q LOSS WILD-TYPE 329  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     14    5
  17Q LOSS WILD-TYPE  329   72
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               14                329
  1                5                 72
[1] 2 2
[1] FALSE
D70V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    16   3
  17Q LOSS WILD-TYPE 374  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     16    3
  17Q LOSS WILD-TYPE  374   56
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                16                374
  YES                3                 56
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    20   0
  17Q LOSS WILD-TYPE 458  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     20    0
  17Q LOSS WILD-TYPE  458   14
                                        clus
vv                                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  20                458
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED     7  11   0   1
  17Q LOSS WILD-TYPE 306 133   5  14
D70V7, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                7                306
  R1               11                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"
D70V8, continuous
D70V9, continuous
D70V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0     3
  17Q LOSS WILD-TYPE     2                         7   143
D70V11, 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    65   2
  18P LOSS WILD-TYPE 418   7
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                425 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                  7 
$`18P LOSS MUTATED`
TCGA-CH-5772 TCGA-CH-5791 TCGA-HC-7821 TCGA-HC-A76W TCGA-KC-A7FA TCGA-KK-A7B4 
       15.98        33.01        31.43         7.00        19.66        32.45 
TCGA-KK-A8IB TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5788 
        2.73        45.14        11.51        35.01         0.92        26.99 
TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-7781 TCGA-EJ-8472 TCGA-EJ-A65B 
       60.13        69.63        64.50        35.28        24.85        23.34 
TCGA-EJ-A7NF TCGA-G9-6354 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-7523 TCGA-G9-A9S0 
        8.22        67.92        26.66        31.50        28.18        26.01 
TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7736 
       23.93        65.26        40.14        40.08        32.91        36.26 
TCGA-HC-7745 TCGA-HC-7820 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A8CY 
       23.70        24.56        22.36         1.78         2.01         9.53 
TCGA-HC-A9TE TCGA-HI-7168 TCGA-HI-7170 TCGA-J9-A8CL TCGA-KK-A59Z TCGA-KK-A6DY 
       19.30       109.25        82.92        13.32        86.40       141.21 
TCGA-KK-A6E7 TCGA-KK-A8I7 TCGA-KK-A8II TCGA-M7-A724 TCGA-TP-A8TV TCGA-V1-A8MJ 
       90.74        65.82       113.98        29.23        20.05        58.88 
TCGA-V1-A8WV TCGA-V1-A9ZI TCGA-VN-A88P TCGA-VP-A872 TCGA-WW-A8ZI TCGA-XJ-A83G 
       22.55        53.92        41.42       119.38        14.76        48.03 
TCGA-XK-AAIV TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A8SO 
       37.25        49.02        48.72        75.75        45.86       114.38 
TCGA-YL-A9WK TCGA-ZG-A9L2 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       70.22        37.94        29.85        20.28        19.17        12.43 
TCGA-ZG-A9LU 
       19.04 

$`18P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-EJ-5542 TCGA-EJ-7123 
        1.02        12.00         1.02        32.02        49.74        84.56 
TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J 
       36.13        35.18        36.76        21.60        21.96        14.83 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-A6AQ TCGA-J4-A83N 
       28.70        39.39        44.55        26.04         3.48        32.61 
TCGA-J9-A8CN TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       40.67         6.44        29.56        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        55.92        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       44.84        41.82        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-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       13.02        31.00         2.04        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 
       15.06        24.03         2.04        13.02         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5521 TCGA-EJ-5522 
       56.98        60.23        62.10        62.10        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        38.37        25.87        25.68        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       28.24        36.33        45.90         3.75        42.94        32.32 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E 
       77.16        76.41        38.10        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       25.74        23.80        21.96        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       21.90         7.56        11.61        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        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       68.68        49.81        67.33        50.70        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       38.01        40.31        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-H9-7775 TCGA-H9-A6BX 
       27.91        30.97        35.44        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        69.53        38.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7737 
       14.47        28.54        28.60        30.87        38.17        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7749 
       31.69        23.57        30.84        17.46        24.59        23.80 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-8213 
       17.16        25.71        30.51        30.84        17.85        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        27.85        30.38        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        15.55         0.76 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH TCGA-HI-7169 
        4.41         4.93        25.48        18.84        27.75        88.24 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
        5.85        10.62        10.55        15.22        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-A6E0 
        8.88        11.57       113.10        83.34        64.70        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       21.96        31.79        32.91        63.48        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       26.43        82.36        66.18        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12         0.89        17.29        47.64        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        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        35.44         6.64        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         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-A875 
       25.18        15.81        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       102.90        23.93        89.49        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ 
       66.97        21.80        58.32        42.94        44.88        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       32.19        12.36        37.05        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
        2.99        31.99        31.96        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 
       17.29         4.87        52.96        51.45        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-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       46.29        32.45        77.79        68.48         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        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       14.53        13.28        10.13         4.27        11.67        42.81 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       36.43        22.59         3.78        16.96        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 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.92               0.76 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            141.21             165.17 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             32.45              30.38 
[1] "0.9 - 141.2 (32.5)" "0.8 - 165.2 (30.4)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                  T2  T3  T4
  18P LOSS MUTATED    17  46   4
  18P LOSS WILD-TYPE 170 242   6
D71V3, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T2               17                170
  T3               46                242
  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 297  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     46   16
  18P LOSS WILD-TYPE  297   61
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               46                297
  1               16                 61
[1] 2 2
[1] FALSE
D71V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    48  12
  18P LOSS WILD-TYPE 342  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     48   12
  18P LOSS WILD-TYPE  342   47
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                48                342
  YES               12                 47
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    64   3
  18P LOSS WILD-TYPE 414  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     64    3
  18P LOSS WILD-TYPE  414   11
                                        clus
vv                                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  64                414
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                3                 11
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    34  31   0   0
  18P LOSS WILD-TYPE 279 113   5  15
D71V7, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               34                279
  R1               31                113
  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"
D71V8, continuous
D71V9, continuous
D71V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         0    21
  18P LOSS WILD-TYPE     2                         7   125
D71V11, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   21                125
[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    98   2
  18Q LOSS WILD-TYPE 385   7
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               100                392 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  7 
$`18Q LOSS MUTATED`
TCGA-CH-5772 TCGA-CH-5791 TCGA-HC-7821 TCGA-HC-A76W TCGA-KC-A7FA TCGA-KK-A7B4 
       15.98        33.01        31.43         7.00        19.66        32.45 
TCGA-KK-A8IB TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5761 
        2.73        45.14        11.51        35.01         2.04         0.92 
TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5524 TCGA-EJ-5525 
       46.92        47.90        60.13        69.63        61.87        36.66 
TCGA-EJ-7781 TCGA-EJ-7794 TCGA-EJ-8472 TCGA-EJ-A65B TCGA-EJ-A7NF TCGA-EJ-A7NH 
       35.28        42.94        24.85        23.34         8.22        15.58 
TCGA-G9-6329 TCGA-G9-6348 TCGA-G9-6354 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       41.62        49.81        67.92        26.66        31.50        37.97 
TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7211 
       30.97        28.18        26.01        69.53        65.26        40.14 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7820 TCGA-HC-A48F 
       40.08        32.91        30.84        23.70        24.56        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6HY TCGA-HC-A8CY TCGA-HC-A9TE TCGA-HI-7168 
        0.76         1.78         4.41         9.53        19.30       109.25 
TCGA-HI-7170 TCGA-J4-A67N TCGA-J9-A8CL TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY 
       82.92        30.81        13.32        83.34        86.40       141.21 
TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AW TCGA-KK-A8I7 TCGA-KK-A8IH 
       72.26       113.33        90.74        34.65        65.82        66.18 
TCGA-KK-A8II TCGA-M7-A724 TCGA-M7-A725 TCGA-TP-A8TV TCGA-V1-A8MJ TCGA-V1-A8MU 
      113.98        29.23        18.84        20.05        58.88        61.68 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A9O7 TCGA-V1-A9ZI TCGA-VN-A88K TCGA-VN-A88P 
       22.55        35.44        82.16        53.92        25.51        41.42 
TCGA-VP-A872 TCGA-VP-A87C TCGA-WW-A8ZI TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XK-AAIV 
      119.38        55.56        14.76        37.05        48.03        37.25 
TCGA-XK-AAJT TCGA-Y6-A9XI TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8SA 
       47.15        17.29        49.02        48.72        75.75        16.83 
TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WK 
       45.86       114.38        68.48         8.98        14.04        70.22 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       49.91        36.10        29.85        20.28        19.17        12.43 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9N3 
       16.96        19.04        22.75        11.47 

$`18Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-EJ-5542 TCGA-EJ-7123 
        1.02        12.00         1.02        32.02        49.74        84.56 
TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J 
       36.13        35.18        36.76        21.60        21.96        14.83 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-A6AQ TCGA-J4-A83N 
       28.70        39.39        44.55        26.04         3.48        32.61 
TCGA-J9-A8CN TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       40.67         6.44        29.56        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        55.92        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       44.84        41.82        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-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       13.02        31.00        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 
       46.52        44.88        38.50        45.73        30.31        45.40 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 
       64.60        48.13        62.04        48.53        56.98        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5526 
       62.10        62.10        64.50        74.93        68.35        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35        27.68         6.28        24.39        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        45.90 
TCGA-EJ-7793 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
        3.75        32.32        77.16        76.41        38.10        25.18 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D 
       20.58        17.23        25.74        23.80        21.96        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NG 
       13.71        18.41        21.90         7.56        11.61        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 
       28.83        22.36        17.23        25.94        20.25        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        80.55 
TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       68.68        67.33        50.70        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       40.31        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        35.44 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        23.93         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-7212 
       38.93        36.36        37.35        14.47        28.54        28.60 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       17.46        24.59        23.80        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 
       27.85        30.38        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       15.88        15.55         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 
        2.33         1.45         1.25         4.93        25.48        18.84 
TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       27.75        88.24        43.69        20.19        40.04        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP 
       13.87         5.85        10.62        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6E0 
        8.65         8.88        11.57       113.10        64.70        48.76 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      165.17        67.59       115.13        68.15        58.19        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       58.36        27.02        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 
       36.13        74.27       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 
       67.46        20.65        62.96        16.21        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN 
       13.15        34.85        25.08         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-V1-A8MF 
      122.17        86.14        18.12         0.89        17.29        47.64 
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        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       15.58         6.64        63.52        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZK TCGA-V1-A9ZR 
       28.73        27.19        17.75        49.87        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q 
        8.84        24.53         6.21        25.18        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       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       89.49        60.92        66.97        21.80        58.32        42.94 
TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83H TCGA-XJ-A9DI 
       44.88        45.47        32.19        12.36        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       41.39        36.95        51.81         4.80        25.32        32.61 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SB 
        4.87        52.96        51.45        62.14        60.56        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        53.06        46.29        32.45 
TCGA-YL-A8SP TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-ZG-A8QW TCGA-ZG-A8QX 
       77.79        53.36        60.99        24.33         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       13.28        10.13         4.27        11.67        42.81        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       36.43        22.59         3.78        12.16        17.98        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.76               0.89 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            141.21             165.17 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            34.830             28.915 
[1] "0.8 - 141.2 (34.8)" "0.9 - 165.2 (28.9)"
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                  T2  T3  T4
  18Q LOSS MUTATED    24  71   4
  18Q LOSS WILD-TYPE 163 217   6
D72V3, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T2               24                163
  T3               71                217
  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    62  29
  18Q LOSS WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     62   29
  18Q LOSS WILD-TYPE  281   48
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               62                281
  1               29                 48
[1] 2 2
[1] FALSE
D72V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    72  18
  18Q LOSS WILD-TYPE 318  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     72   18
  18Q LOSS WILD-TYPE  318   41
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                72                318
  YES               18                 41
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    97   3
  18Q LOSS WILD-TYPE 381  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     97    3
  18Q LOSS WILD-TYPE  381   11
                                        clus
vv                                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  97                381
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                3                 11
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    47  49   0   2
  18Q LOSS WILD-TYPE 266  95   5  13
D72V7, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               47                266
  R1               49                 95
  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"
D72V8, continuous
D72V9, continuous
D72V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         2    27
  18Q LOSS WILD-TYPE     2                         5   119
D72V11, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   27                119
[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    19   0
  19P LOSS WILD-TYPE 464   9
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                473 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 0                  9 
$`19P LOSS MUTATED`
TCGA-KC-A7FA TCGA-EJ-5525 TCGA-EJ-7328 TCGA-EJ-7781 TCGA-HC-7080 TCGA-J9-A52B 
       19.66        36.66        27.68        35.28        36.36        13.87 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-TP-A8TV 
       10.62        13.32        68.15       113.33        90.74        20.05 
TCGA-V1-A9O7 TCGA-XK-AAJA TCGA-YL-A8HM TCGA-YL-A8SL TCGA-YL-A9WK TCGA-ZG-A9M4 
       82.16        30.58        48.72        32.45        70.22        17.98 
TCGA-ZG-A9NI 
        4.34 

$`19P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP 
       31.43         3.48         7.00        32.61        40.67         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       74.93        68.35        61.87        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7330 
       33.14        25.35        33.83        27.09        30.35         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        38.37        25.87        25.68        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       28.24        36.33        45.90         3.75        42.94        32.32 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       77.16        76.41        38.10        24.85        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         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        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        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        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        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        35.44        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       65.26        38.93        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        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 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CK TCGA-J9-A8CM 
       18.18        13.55        27.12         5.85        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.59       115.13        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        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-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        67.46        20.65        62.96        16.21 
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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12         0.89        17.29        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 
       15.58        22.55        35.44         6.64        63.52        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJP TCGA-XK-AAJR 
       31.99        31.96        37.25        40.04        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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        75.75        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        77.79        68.48 
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 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        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 
       12.16        22.75        14.96        11.47        13.48 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              4.34               0.76 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            113.33             165.17 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             32.45              30.51 
[1] "4.3 - 113.3 (32.5)" "0.8 - 165.2 (30.5)"
[1] "hr="     "2.6e+07"
D73V2, continuous
                    vv
clus                  T2  T3  T4
  19P LOSS MUTATED     4  15   0
  19P LOSS WILD-TYPE 183 273  10
D73V3, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T2                4                183
  T3               15                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"
D73V4, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    15   3
  19P LOSS WILD-TYPE 328  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     15    3
  19P LOSS WILD-TYPE  328   74
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               15                328
  1                3                 74
[1] 2 2
[1] FALSE
D73V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    15   3
  19P LOSS WILD-TYPE 375  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     15    3
  19P LOSS WILD-TYPE  375   56
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                15                375
  YES                3                 56
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    19   0
  19P LOSS WILD-TYPE 459  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     19    0
  19P LOSS WILD-TYPE  459   14
                                        clus
vv                                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  19                459
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    10   9   0   0
  19P LOSS WILD-TYPE 303 135   5  15
D73V7, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               10                303
  R1                9                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"
D73V8, continuous
D73V9, continuous
D73V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         0     4
  19P LOSS WILD-TYPE     2                         7   142
D73V11, multiclass
                           clus
vv                          19P LOSS MUTATED 19P 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(74) Variable = 19Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    18   0
  19Q LOSS WILD-TYPE 465   9
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                18                474 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                  9 
$`19Q LOSS MUTATED`
TCGA-KC-A7FA TCGA-EJ-7328 TCGA-EJ-7781 TCGA-HC-7080 TCGA-J9-A52B TCGA-J9-A52E 
       19.66        27.68        35.28        36.36        13.87        10.62 
TCGA-J9-A8CL TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-TP-A8TV TCGA-V1-A9O7 
       13.32        68.15       113.33        90.74        20.05        82.16 
TCGA-XK-AAJA TCGA-YL-A8HM TCGA-YL-A8SL TCGA-YL-A9WK TCGA-ZG-A9M4 TCGA-ZG-A9NI 
       30.58        48.72        32.45        70.22        17.98         4.34 

$`19Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP 
       31.43         3.48         7.00        32.61        40.67         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        30.35 
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        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
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-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
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        28.83        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       25.94        20.25        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        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        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        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       69.53        65.26        38.93        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        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        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       19.30        27.75       109.25        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        40.04        33.01        25.32        30.94        30.81 
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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CK 
       17.85        18.18        13.55        27.12         5.85        10.55 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
      165.17        67.59       115.13        58.19        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        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        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        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12         0.89        17.29        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 
       30.38        15.58        22.55        35.44         6.64        63.52 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58       102.90 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        89.49        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 
       58.32        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 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJP 
        2.99        31.99        31.96        37.25        40.04        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       17.29         4.87        52.96        49.02        51.45        75.75 
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        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL 
       68.48         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        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        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-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        22.75        14.96        11.47        13.48 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              4.34               0.76 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            113.33             165.17 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            31.515             30.610 
[1] "4.3 - 113.3 (31.5)" "0.8 - 165.2 (30.6)"
[1] "hr="     "2.6e+07"
D74V2, continuous
                    vv
clus                  T2  T3  T4
  19Q LOSS MUTATED     3  15   0
  19Q LOSS WILD-TYPE 184 273  10
D74V3, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T2                3                184
  T3               15                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"
D74V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    14   3
  19Q LOSS WILD-TYPE 329  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     14    3
  19Q LOSS WILD-TYPE  329   74
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               14                329
  1                3                 74
[1] 2 2
[1] FALSE
D74V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    14   3
  19Q LOSS WILD-TYPE 376  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     14    3
  19Q LOSS WILD-TYPE  376   56
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                14                376
  YES                3                 56
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    18   0
  19Q LOSS WILD-TYPE 460  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     18    0
  19Q LOSS WILD-TYPE  460   14
                                        clus
vv                                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  18                460
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED     9   9   0   0
  19Q LOSS WILD-TYPE 304 135   5  15
D74V7, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                9                304
  R1                9                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"
D74V8, continuous
D74V9, continuous
D74V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0     3
  19Q LOSS WILD-TYPE     2                         7   143
D74V11, 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    18   1
  20P LOSS WILD-TYPE 465   8
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                473 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  8 
$`20P LOSS MUTATED`
TCGA-CH-5772 TCGA-EJ-7312 TCGA-HC-7821 TCGA-EJ-5532 TCGA-EJ-7314 TCGA-EJ-7784 
       15.98        36.13        31.43        60.10        37.81        25.68 
TCGA-FC-A4JI TCGA-G9-6339 TCGA-G9-6494 TCGA-G9-A9S0 TCGA-HC-7077 TCGA-KK-A8IJ 
       28.83        83.87        58.22        26.01        69.53        51.25 
TCGA-KK-A8IK TCGA-V1-A8WW TCGA-V1-A9Z7 TCGA-VP-A87C TCGA-YL-A8SL TCGA-ZG-A9L0 
       67.46        35.44        28.73        55.56        32.45        11.67 
TCGA-ZG-A9LS 
       16.96 

$`20P LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
        1.02        12.00         1.02        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J 
       84.56        35.18        36.76        21.60        21.96        14.83 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-A6AQ TCGA-HC-A76W 
       28.70        39.39        44.55        26.04         3.48         7.00 
TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 
       32.61        40.67        19.66         6.44        29.56        32.45 
TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
        2.73        41.00        41.49        32.19        20.42        55.92 
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       45.14        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       41.82        20.22        11.51         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-5754 TCGA-CH-5761 TCGA-CH-5762 
       13.02        35.01        31.00         2.04         0.92        44.02 
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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       26.99         9.99         2.99        29.00        48.56        57.86 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        56.55        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        46.92        30.31        45.40        47.90        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        62.76        58.45        60.23        41.85 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       88.34        93.70        83.57        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       27.09        30.35        27.68         6.28        24.39        35.28 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.87        38.70        36.03        28.24        36.33 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
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-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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        25.94        20.25        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       81.04        67.99        66.67        55.76        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        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-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       25.15        27.29        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        35.44        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 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        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 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       18.18        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        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-A7FD 
       19.96        44.35        43.66        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        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        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-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
      113.98        20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        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        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       35.08        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
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       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87D 
       75.91       109.58       102.90        23.93        89.49        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        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        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         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        75.75        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-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        46.29       114.38        77.79        68.48         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        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        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 TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             11.67               0.76 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             83.87             165.17 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             35.44              30.38 
[1] "11.7 - 83.9 (35.4)" "0.8 - 165.2 (30.4)"
[1] "hr=" "3.4"
D75V2, continuous
                    vv
clus                  T2  T3  T4
  20P LOSS MUTATED     3  15   1
  20P LOSS WILD-TYPE 184 273   9
D75V3, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T2                3                184
  T3               15                273
  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   7
  20P LOSS WILD-TYPE 333  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     10    7
  20P LOSS WILD-TYPE  333   70
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               10                333
  1                7                 70
[1] 2 2
[1] FALSE
D75V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    13   5
  20P LOSS WILD-TYPE 377  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     13    5
  20P LOSS WILD-TYPE  377   54
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                13                377
  YES                5                 54
[1] 2 2
[1] FALSE
D75V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    19   0
  20P LOSS WILD-TYPE 459  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     19    0
  20P LOSS WILD-TYPE  459   14
                                        clus
vv                                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  19                459
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    13   5   0   0
  20P LOSS WILD-TYPE 300 139   5  15
D75V7, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               13                300
  R1                5                139
  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"
D75V8, continuous
D75V9, continuous
D75V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         1     6
  20P LOSS WILD-TYPE     2                         6   140
D75V11, 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 475   9
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                484 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 0                  9 
$`20Q LOSS MUTATED`
TCGA-CH-5772 TCGA-EJ-5532 TCGA-EJ-7784 TCGA-FC-A4JI TCGA-HC-A632 TCGA-V1-A8WW 
       15.98        60.10        25.68        28.83         2.01        35.44 
TCGA-V1-A9Z7 TCGA-YL-A8SL 
       28.73        32.45 

$`20Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
        1.02        12.00         1.02        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       60.23        41.85        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
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-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
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        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        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        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        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        35.44        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        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        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        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 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       18.18        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        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-A7FD 
       19.96        44.35        43.66        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        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        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        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        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-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        67.46        20.65        62.96        16.21 
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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
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        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       15.65        37.28        35.08        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
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        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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 
       75.75        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 
       77.79        68.48         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 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       13.28        10.13         4.27        11.67        42.81        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 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.01               0.76 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             60.10             165.17 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             28.78              30.76 
[1] "2.0 - 60.1 (28.8)"  "0.8 - 165.2 (30.8)"
[1] "hr="     "9100000"
D76V2, continuous
                    vv
clus                  T2  T3  T4
  20Q LOSS MUTATED     1   7   0
  20Q LOSS WILD-TYPE 186 281  10
D76V3, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T2                1                186
  T3                7                281
  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"
D76V4, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   2
  20Q LOSS WILD-TYPE 338  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    2
  20Q LOSS WILD-TYPE  338   75
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                5                338
  1                2                 75
[1] 2 2
[1] FALSE
D76V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   2
  20Q LOSS WILD-TYPE 385  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    2
  20Q LOSS WILD-TYPE  385   57
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 5                385
  YES                2                 57
[1] 2 2
[1] FALSE
D76V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     8   0
  20Q LOSS WILD-TYPE 470  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      8    0
  20Q LOSS WILD-TYPE  470   14
                                        clus
vv                                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   8                470
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                0                 14
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     7   1   0   0
  20Q LOSS WILD-TYPE 306 143   5  15
D76V7, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                7                306
  R1                1                143
  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"
D76V8, continuous
D76V9, continuous
D76V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     3
  20Q LOSS WILD-TYPE     2                         7   143
D76V11, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q 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(77) Variable = 21Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    24   0
  21Q LOSS WILD-TYPE 459   9
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                24                468 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                  9 
$`21Q LOSS MUTATED`
TCGA-HC-7748 TCGA-HC-7821 TCGA-KC-A7FA TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 
       26.04        31.43        19.66        45.14        11.51        35.01 
TCGA-CH-5761 TCGA-EJ-5519 TCGA-EJ-8472 TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-G9-6329 
        0.92        64.50        24.85         8.22        15.58        41.62 
TCGA-G9-7521 TCGA-J9-A52B TCGA-V1-A8WW TCGA-V1-A9O7 TCGA-VP-A87K TCGA-XK-AAIW 
       30.97        13.87        35.44        82.16        42.94        40.04 
TCGA-YL-A8SJ TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A9KY TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       45.86        24.33        36.10         4.27        17.98        11.47 

$`21Q LOSS WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-A6AQ 
       21.96        14.83        28.70        39.39        44.55         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 
        7.00        32.61        40.67         6.44        29.56        32.45 
TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
        2.73        41.00        41.49        32.19        20.42        55.92 
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        45.30         3.68        28.37        44.84        41.82 
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-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        2.04        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 
       60.13        60.23        62.10        62.10        69.63        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        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        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       42.94        32.32        77.16        76.41        38.10        25.18 
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-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
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        28.83        22.36        17.23        25.94        20.25 
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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
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        35.44 
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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
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        27.85        30.38 
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        15.55 
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-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
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        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        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-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12         5.85        10.62        10.55        13.32        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        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        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        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-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        63.52        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
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        25.18        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       119.38        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        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        58.32        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        12.36        37.05        48.03        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        37.25        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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        75.75        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-A8SL 
       41.46        45.14        28.77        53.06        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        77.79        68.48         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       60.99        70.22        49.91         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
       10.13        11.67        42.81        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-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       19.04        12.16        22.75        14.96        13.48         4.34 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.92               0.76 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             82.16             165.17 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            28.505             30.645 
[1] "0.9 - 82.2 (28.5)"  "0.8 - 165.2 (30.6)"
[1] "hr="     "2.6e+07"
D77V2, continuous
                    vv
clus                  T2  T3  T4
  21Q LOSS MUTATED     4  17   3
  21Q LOSS WILD-TYPE 183 271   7
D77V3, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T2                4                183
  T3               17                271
  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  10
  21Q LOSS WILD-TYPE 330  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     13   10
  21Q LOSS WILD-TYPE  330   67
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               13                330
  1               10                 67
[1] 2 2
[1] FALSE
D77V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    19   4
  21Q LOSS WILD-TYPE 371  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     19    4
  21Q LOSS WILD-TYPE  371   55
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                19                371
  YES                4                 55
[1] 2 2
[1] FALSE
D77V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    23   1
  21Q LOSS WILD-TYPE 455  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     23    1
  21Q LOSS WILD-TYPE  455   13
                                        clus
vv                                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  23                455
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                1                 13
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED    12  11   0   0
  21Q LOSS WILD-TYPE 301 133   5  15
D77V7, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               12                301
  R1               11                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"
D77V8, continuous
D77V9, continuous
D77V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       0                         0     6
  21Q LOSS WILD-TYPE     2                         7   140
D77V11, 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    45   2
  22Q LOSS WILD-TYPE 438   7
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                47                445 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                  7 
$`22Q LOSS MUTATED`
TCGA-CH-5753 TCGA-CH-5772 TCGA-2A-A8VT TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5766 
        1.02        15.98        45.14        35.01         0.92         1.02 
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       109.25        43.69        10.62 
TCGA-J9-A8CL TCGA-KK-A8IG TCGA-M7-A71Y TCGA-M7-A725 TCGA-V1-A8MJ TCGA-V1-A8WW 
       13.32        82.36        16.21        18.84        58.88        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9OL TCGA-VN-A88K TCGA-VP-A872 TCGA-VP-A875 
        6.64        82.16        62.89        25.51       119.38        75.91 
TCGA-VP-A87K TCGA-XJ-A9DX TCGA-XK-AAJA TCGA-XQ-A8TA TCGA-YL-A8HM TCGA-YL-A8SB 
       42.94        31.99        30.58         4.80        48.72        56.52 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WK TCGA-YL-A9WL TCGA-ZG-A8QW TCGA-ZG-A9L9 
       68.48        14.04        70.22        24.33         3.09        20.28 
TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       12.43        19.04        17.98        14.96        11.47 

$`22Q LOSS WILD-TYPE`
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 TCGA-EJ-7123 
       12.00         1.02        32.02        33.01        49.74        84.56 
TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J 
       36.13        35.18        36.76        21.60        21.96        14.83 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ 
       28.70        39.39        44.55        26.04        31.43         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 
        7.00        32.61        40.67        19.66         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       55.92        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       41.82        20.22        11.51         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-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5767 
       13.02        31.00         2.04        44.02        23.01        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 
       45.40        47.90        64.60        48.13        62.04        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7784 
       27.68         6.28        24.39        35.28        38.37        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       42.94        32.32        77.16        76.41        38.10        25.18 
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-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
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        28.83        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       25.94        20.25        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        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       67.33        50.70        67.92        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        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-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        35.44        28.18        32.68        26.01        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       38.93        37.35        14.47        28.54        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       24.56        19.36        28.27        23.87        27.85        30.38 
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        15.55 
TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        0.76         2.01         2.20         1.61        17.42         2.33 
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-HC-A9TE TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
       18.84        19.30        27.75        88.24        82.92        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        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        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CK 
       18.18        13.55        27.12        13.87         5.85        10.55 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        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 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
       21.96        65.82        31.79        32.91        63.48        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       69.27        26.43        66.18       113.98        51.25        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65        62.96        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08        29.23         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       28.18        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA 
       30.38        15.58        22.55        63.52        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       38.93        79.00        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
       44.75         8.84        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 
       41.42        44.91        25.78        16.31       109.58       102.90 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        89.49        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 
       58.32        44.88        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        37.25        40.04        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
       51.81        25.32        32.61        17.29         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        75.75        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-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ 
       32.45       114.38        77.79         8.98        53.36        60.99 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       49.91        36.10        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9ND 
       19.17         3.78        16.96        12.16        22.75        13.48 
TCGA-ZG-A9NI 
        4.34 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.92               0.76 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            119.38             165.17 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             25.51              30.84 
[1] "0.9 - 119.4 (25.5)" "0.8 - 165.2 (30.8)"
[1] "hr=" "2.6"
D78V2, continuous
                    vv
clus                  T2  T3  T4
  22Q LOSS MUTATED     5  39   2
  22Q LOSS WILD-TYPE 182 249   8
D78V3, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T2                5                182
  T3               39                249
  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  17
  22Q LOSS WILD-TYPE 316  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     27   17
  22Q LOSS WILD-TYPE  316   60
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               27                316
  1               17                 60
[1] 2 2
[1] FALSE
D78V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    30  11
  22Q LOSS WILD-TYPE 360  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     30   11
  22Q LOSS WILD-TYPE  360   48
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                30                360
  YES               11                 48
[1] 2 2
[1] FALSE
D78V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    45   2
  22Q LOSS WILD-TYPE 433  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     45    2
  22Q LOSS WILD-TYPE  433   12
                                        clus
vv                                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  45                433
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                2                 12
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    22  24   0   0
  22Q LOSS WILD-TYPE 291 120   5  15
D78V7, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               22                291
  R1               24                120
  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"
D78V8, continuous
D78V9, continuous
D78V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       0                         1    10
  22Q LOSS WILD-TYPE     2                         6   136
D78V11, 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   2
  XP LOSS WILD-TYPE 447   7
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               38               454 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                2                 7 
$`XP LOSS MUTATED`
TCGA-CH-5753 TCGA-EJ-7312 TCGA-EJ-5507 TCGA-EJ-7783 TCGA-EJ-7789 TCGA-EJ-A65D 
        1.02        36.13        47.90        25.87        36.33        12.92 
TCGA-G9-6369 TCGA-G9-6499 TCGA-HC-7213 TCGA-HC-A48F TCGA-HC-A8CY TCGA-HC-A9TE 
       39.95        50.73        40.08        22.36         9.53        19.30 
TCGA-HI-7171 TCGA-J4-A67N TCGA-J9-A8CL TCGA-KK-A59X TCGA-KK-A6E0 TCGA-KK-A6E1 
       43.69        30.81        13.32        83.34        48.76        72.26 
TCGA-KK-A6E8 TCGA-KK-A8IA TCGA-KK-A8IH TCGA-TP-A8TV TCGA-V1-A9O5 TCGA-V1-A9O9 
       58.19        63.48        66.18        20.05        63.52        94.36 
TCGA-VN-A943 TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XK-AAJP TCGA-XQ-A8TA 
       16.31        42.94        44.88        14.76        41.39         4.80 
TCGA-YL-A8SC TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A9WL TCGA-ZG-A9KY TCGA-ZG-A9LM 
       41.46        46.29        32.45        24.33         4.27        12.43 
TCGA-ZG-A9M4 TCGA-ZG-A9ND 
       17.98        13.48 

$`XP LOSS WILD-TYPE`
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
       12.00         1.02        15.98        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J 
       84.56        35.18        36.76        21.60        21.96        14.83 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ 
       28.70        39.39        44.55        26.04        31.43         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 
        7.00        32.61        40.67        19.66         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       38.50        45.73        46.92        30.31        45.40        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        35.28        38.37        25.68        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       28.24        45.90         3.75        42.94        32.32        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F 
       25.74        23.80        21.96        23.34        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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 
       28.83        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       40.18        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-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 
       22.32         1.58        15.88        15.55         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH 
        1.25         4.41         4.93        25.48        18.84        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
      109.25        88.24        82.92        20.19        40.04        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP 
       13.87         5.85        10.62        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z 
        8.65         8.88        11.57       113.10        64.70        86.40 
TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
      141.21       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       90.74        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID 
       21.96        65.82        31.79        32.91        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       26.43        82.36       113.98        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-V1-A8MF 
      122.17        86.14        18.12         0.89        17.29        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 
       64.04        30.38        15.58        22.55        35.44         6.64 
TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       82.16        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TB 
       40.04        30.58        36.95        47.15        51.81        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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        75.75        62.14        60.56        16.83        56.52 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SP 
       45.14        28.77        53.06        45.86       114.38        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       68.48         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       20.28        19.17         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       22.75        14.96        11.47         4.34 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             1.02              0.76 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            94.36            165.17 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            36.23             30.38 
[1] "1.0 - 94.4 (36.2)"  "0.8 - 165.2 (30.4)"
[1] "hr=" "4.7"
D79V2, continuous
                   vv
clus                 T2  T3  T4
  XP LOSS MUTATED     6  29   2
  XP LOSS WILD-TYPE 181 259   8
D79V3, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T2               6               181
  T3              29               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"
D79V4, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    23  13
  XP LOSS WILD-TYPE 320  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     23   13
  XP LOSS WILD-TYPE  320   64
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              23               320
  1              13                64
[1] 2 2
[1] FALSE
D79V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    26   9
  XP LOSS WILD-TYPE 364  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     26    9
  XP LOSS WILD-TYPE  364   50
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               26               364
  YES               9                50
[1] 2 2
[1] FALSE
D79V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    36   2
  XP LOSS WILD-TYPE 442  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     36    2
  XP LOSS WILD-TYPE  442   12
                                        clus
vv                                       XP LOSS MUTATED XP LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 36               442
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               2                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    20  14   0   3
  XP LOSS WILD-TYPE 293 130   5  12
D79V7, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              20               293
  R1              14               130
  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"
D79V8, continuous
D79V9, continuous
D79V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       0                         1     7
  XP LOSS WILD-TYPE     2                         6   139
D79V11, 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   2
  XQ LOSS WILD-TYPE 447   7
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               38               454 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                 7 
$`XQ LOSS MUTATED`
TCGA-CH-5753 TCGA-EJ-7312 TCGA-EJ-5507 TCGA-EJ-7783 TCGA-EJ-7789 TCGA-EJ-A65D 
        1.02        36.13        47.90        25.87        36.33        12.92 
TCGA-G9-6369 TCGA-G9-6499 TCGA-HC-7213 TCGA-HC-A48F TCGA-HC-A8CY TCGA-HC-A9TE 
       39.95        50.73        40.08        22.36         9.53        19.30 
TCGA-HI-7171 TCGA-J4-A67N TCGA-J9-A8CL TCGA-KK-A59X TCGA-KK-A6E0 TCGA-KK-A6E1 
       43.69        30.81        13.32        83.34        48.76        72.26 
TCGA-KK-A6E8 TCGA-KK-A8IA TCGA-KK-A8IH TCGA-TP-A8TV TCGA-V1-A9O5 TCGA-V1-A9O9 
       58.19        63.48        66.18        20.05        63.52        94.36 
TCGA-VN-A943 TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XK-AAJP TCGA-XQ-A8TA 
       16.31        42.94        44.88        14.76        41.39         4.80 
TCGA-YL-A8SC TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A9WL TCGA-ZG-A9KY TCGA-ZG-A9LM 
       41.46        46.29        32.45        24.33         4.27        12.43 
TCGA-ZG-A9M4 TCGA-ZG-A9ND 
       17.98        13.48 

$`XQ LOSS WILD-TYPE`
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
       12.00         1.02        15.98        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J 
       84.56        35.18        36.76        21.60        21.96        14.83 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ 
       28.70        39.39        44.55        26.04        31.43         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 
        7.00        32.61        40.67        19.66         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        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-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       38.50        45.73        46.92        30.31        45.40        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        35.28        38.37        25.68        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       28.24        45.90         3.75        42.94        32.32        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F 
       25.74        23.80        21.96        23.34        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         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 
       28.83        22.36        17.23        25.94        20.25        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 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       40.18        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-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        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-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        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        27.85        30.38        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 
       22.32         1.58        15.88        15.55         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TH 
        1.25         4.41         4.93        25.48        18.84        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
      109.25        88.24        82.92        20.19        40.04        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-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP 
       13.87         5.85        10.62        10.55        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-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z 
        8.65         8.88        11.57       113.10        64.70        86.40 
TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
      141.21       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       90.74        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8ID 
       21.96        65.82        31.79        32.91        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       26.43        82.36       113.98        51.25        67.46        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        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-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-V1-A8MF 
      122.17        86.14        18.12         0.89        17.29        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 
       64.04        30.38        15.58        22.55        35.44         6.64 
TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       82.16        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         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        25.18        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       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        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-AAJA TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TB 
       40.04        30.58        36.95        47.15        51.81        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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        75.75        62.14        60.56        16.83        56.52 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SP 
       45.14        28.77        53.06        45.86       114.38        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       68.48         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       20.28        19.17         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       22.75        14.96        11.47         4.34 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             1.02              0.76 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            94.36            165.17 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            36.23             30.38 
[1] "1.0 - 94.4 (36.2)"  "0.8 - 165.2 (30.4)"
[1] "hr=" "4.7"
D80V2, continuous
                   vv
clus                 T2  T3  T4
  XQ LOSS MUTATED     6  29   2
  XQ LOSS WILD-TYPE 181 259   8
D80V3, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T2               6               181
  T3              29               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"
D80V4, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    23  13
  XQ LOSS WILD-TYPE 320  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     23   13
  XQ LOSS WILD-TYPE  320   64
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              23               320
  1              13                64
[1] 2 2
[1] FALSE
D80V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    26   9
  XQ LOSS WILD-TYPE 364  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     26    9
  XQ LOSS WILD-TYPE  364   50
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               26               364
  YES               9                50
[1] 2 2
[1] FALSE
D80V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    36   2
  XQ LOSS WILD-TYPE 442  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     36    2
  XQ LOSS WILD-TYPE  442   12
                                        clus
vv                                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 36               442
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               2                12
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    20  14   0   3
  XQ LOSS WILD-TYPE 293 130   5  12
D80V7, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              20               293
  R1              14               130
  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"
D80V8, continuous
D80V9, continuous
D80V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       0                         1     7
  XQ LOSS WILD-TYPE     2                         6   139
D80V11, 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"
