[1] "ofn"       "-oTLGG-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/LGG-TP/15082624/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/15087637/transformed.cor.cli.txt"

nPatients in clinical file=475, in cluster file=513, common to both=472
[1] "Reduce the number of clustering variables from 82 to 80."
[1]  80 472
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               461 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               461 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               20               452 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               20               452 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13               459 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13               459 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12               460 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12               460 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               461 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               461 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               464 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               464 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               461 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               461 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               467 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               467 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9               463 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9               463 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               466 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               466 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               465 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               465 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              110               362 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              110               362 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              141               331 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              141               331 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               43               429 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               43               429 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               51               421 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               51               421 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               457 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               457 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               22               450 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               22               450 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                53                419 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                53                419 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 9                463 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 9                463 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                30                442 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                30                442 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                56                416 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                56                416 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                30                442 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                30                442 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                14                458 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                14                458 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                466 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                466 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                469 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                469 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                463 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                463 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                456 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                456 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                454 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                454 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                18                454 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                18                454 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                20                452 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                20                452 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                457 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                457 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                462 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                462 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                91                381 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                91                381 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                450 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                450 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                38                434 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                38                434 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                38                434 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                38                434 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                23                449 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                23                449 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                455 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                455 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18               454 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18               454 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               34               438 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               34               438 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              171               301 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              171               301 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               24               448 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               24               448 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               19               453 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               19               453 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               456 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               456 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               26               446 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               26               446 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               25               447 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               25               447 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               63               409 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               63               409 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               82               390 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               82               390 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               33               439 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               33               439 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               439 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               439 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               26               446 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               26               446 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               55               417 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               55               417 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               469 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               469 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               469 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               469 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               15               457 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               15               457 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               463 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               463 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              104               368 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              104               368 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               44               428 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               44               428 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                74                398 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                74                398 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                87                385 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                87                385 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                57                415 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                57                415 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                20                452 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                20                452 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                24                448 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                24                448 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                46                426 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                46                426 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               105                367 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               105                367 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                70                402 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                70                402 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                46                426 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                46                426 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                461 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                461 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                19                453 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                19                453 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                460 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                460 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                464 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                464 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                63                409 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                63                409 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                58                414 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                58                414 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                450 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                450 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               193                279 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               193                279 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                467 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                467 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                443 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                443 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                50                422 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                50                422 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               89               383 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               89               383 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               65               407 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               65               407 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "DCC_UPLOAD_DATE"                       
 [7] "GENDER"                                
 [8] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
 [9] "DAYS_TO_LAST_KNOWN_ALIVE"              
[10] "RADIATION_THERAPY"                     
[11] "KARNOFSKY_PERFORMANCE_SCORE"           
[12] "HISTOLOGICAL_TYPE"                     
[13] "RADIATIONS_RADIATION_REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCH_NUMBER"                          

Input Data has 16 rows and 472 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=92,	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=354,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 9:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 10:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH_NUMBER':	nDistinctValues=21,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 472 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"                        
[2] "GENDER"                                
[3] "KARNOFSKY_PERFORMANCE_SCORE"           
[4] "HISTOLOGICAL_TYPE"                     
[5] "RADIATIONS_RADIATION_REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     7   4
  1P GAIN WILD-TYPE 369  90
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               459 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                90 
$`1P GAIN MUTATED`
TCGA-CS-4941 TCGA-CS-6665 TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-8165 TCGA-DU-A5TT 
        7.69        12.43        14.99        10.36        19.13         4.96 
TCGA-E1-5304 TCGA-HT-7686 TCGA-HT-A4DS TCGA-S9-A6WM TCGA-TM-A84I 
       41.13        42.74         0.23        19.86        28.08 

$`1P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 
        8.84       117.40        90.77        30.67        26.30         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59        15.12         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       28.27        15.72        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.14        16.83        21.40        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       80.12        32.45        84.99        31.10        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       59.05        40.64        30.44        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.23              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            42.74            211.17 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            14.99             18.71 
[1] "0.2 - 42.7 (15.0)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "3.4"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     7   4
  1P GAIN WILD-TYPE 199 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      7    4
  1P GAIN WILD-TYPE  199  262
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               7               199
  MALE                 4               262
[1] 2 2
[1] FALSE
D1V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1P GAIN MUTATED             9                0                 2
  1P GAIN WILD-TYPE         167              118               176
D1V5, multiclass
                   clus
vv                  1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASTROCYTOMA                     9               167
  OLIGOASTROCYTOMA                0               118
  OLIGODENDROGLIOMA               2               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     3   8
  1P GAIN WILD-TYPE  89 372
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    8
  1P GAIN WILD-TYPE   89  372
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                3                89
  YES               8               372
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     0
  1P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           0    11
  1P GAIN WILD-TYPE                        15   426
D1V7, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         11               426
[1] 4 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, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  11
  1P GAIN WILD-TYPE  18 408
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   11
  1P GAIN WILD-TYPE   18  408
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              11               408
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    14   6
  1Q GAIN WILD-TYPE 362  88
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               20               450 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                88 
$`1Q GAIN MUTATED`
TCGA-CS-4941 TCGA-CS-6665 TCGA-DB-A64L TCGA-DU-6392 TCGA-DU-7010 TCGA-DU-7015 
        7.69        12.43        24.20       211.17        14.99        90.77 
TCGA-DU-7290 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A7TB TCGA-E1-5304 
       10.36        14.60        19.13         4.96        42.31        41.13 
TCGA-HT-7475 TCGA-HT-7688 TCGA-HT-A4DS TCGA-S9-A6WM TCGA-TM-A84B TCGA-TM-A84I 
       17.42        31.69         0.23        19.86        24.92        28.08 
TCGA-VM-A8CA TCGA-WH-A86K 
       13.51        13.32 

$`1Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       31.63        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      156.23       138.28       105.21         6.54         8.84       117.40 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       30.67        26.30         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
        5.10        23.74        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       77.88        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
        0.03        16.54         3.75         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       28.27        15.72        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.14        16.83        21.40        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       80.12        32.45        84.99        31.10        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       48.33        49.32        34.78        48.39        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       40.64        30.44        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       43.04        30.08         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 
       37.05        16.01        23.21         8.05        51.06        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.23              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           211.17            182.33 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           18.275            18.660 
[1] "0.2 - 211.2 (18.3)" "0.0 - 182.3 (18.7)"
[1] "hr=" "1.4"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    10  10
  1Q GAIN WILD-TYPE 196 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     10   10
  1Q GAIN WILD-TYPE  196  256
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              10               196
  MALE                10               256
[1] 2 2
[1] FALSE
D2V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1Q GAIN MUTATED            11                2                 7
  1Q GAIN WILD-TYPE         165              116               171
D2V5, multiclass
                   clus
vv                  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASTROCYTOMA                    11               165
  OLIGOASTROCYTOMA                2               116
  OLIGODENDROGLIOMA               7               171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     5  15
  1Q GAIN WILD-TYPE  87 365
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   15
  1Q GAIN WILD-TYPE   87  365
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                5                87
  YES              15               365
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     1
  1Q GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           0    18
  1Q GAIN WILD-TYPE                        15   419
D2V7, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         18               419
[1] 4 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, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     0  19
  1Q GAIN WILD-TYPE  18 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   19
  1Q GAIN WILD-TYPE   18  400
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              19               400
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED     9   4
  2P GAIN WILD-TYPE 367  90
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13               457 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                90 
$`2P GAIN MUTATED`
TCGA-DB-5274 TCGA-DH-A669 TCGA-DH-A7UR TCGA-DU-8165 TCGA-E1-5304 TCGA-E1-A7YV 
       75.25        30.21        54.25        19.13        41.13        32.45 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-S9-A6WM TCGA-S9-A7J0 TCGA-TM-A84Q TCGA-VM-A8CA 
       15.72         0.23        19.86        20.02        25.38        13.51 
TCGA-VW-A8FI 
        8.05 

$`2P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       14.60        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
       95.57       130.78        75.02        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       29.59        34.19        28.27        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        31.10        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       23.51         7.13         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       24.79        33.24        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       26.99        43.04        30.08         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K 
       23.47        37.05        16.01        23.21        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.23              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            75.25            211.17 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            20.02             18.61 
[1] "0.2 - 75.2 (20.0)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.7"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     7   6
  2P GAIN WILD-TYPE 199 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      7    6
  2P GAIN WILD-TYPE  199  260
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               7               199
  MALE                 6               260
[1] 2 2
[1] FALSE
D3V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2P GAIN MUTATED             6                2                 5
  2P GAIN WILD-TYPE         170              116               173
D3V5, multiclass
                   clus
vv                  2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASTROCYTOMA                     6               170
  OLIGOASTROCYTOMA                2               116
  OLIGODENDROGLIOMA               5               173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  11
  2P GAIN WILD-TYPE  90 369
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   11
  2P GAIN WILD-TYPE   90  369
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                2                90
  YES              11               369
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     0
  2P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           0    12
  2P GAIN WILD-TYPE                        15   425
D3V7, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         12               425
[1] 4 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, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1  11
  2P GAIN WILD-TYPE  17 408
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1   11
  2P GAIN WILD-TYPE   17  408
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              11               408
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED     9   3
  2Q GAIN WILD-TYPE 367  91
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12               458 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                3                91 
$`2Q GAIN MUTATED`
TCGA-DB-5274 TCGA-DH-A7UR TCGA-DU-8165 TCGA-E1-5304 TCGA-E1-A7YV TCGA-HT-8564 
       75.25        54.25        19.13        41.13        32.45        15.72 
TCGA-HT-A4DS TCGA-S9-A6WM TCGA-S9-A7J0 TCGA-TM-A84Q TCGA-VM-A8CA TCGA-VW-A8FI 
        0.23        19.86        20.02        25.38        13.51         8.05 

$`2Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       27.81        17.19        17.19        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 
       78.21        95.57       130.78        75.02        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 
        0.23        29.59        34.19        28.27        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       22.32        23.51         7.13         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        24.79        33.24        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
       15.98        26.99        43.04        30.08         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       35.93        23.47        37.05        16.01        23.21        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.23              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            75.25            211.17 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            19.94             18.61 
[1] "0.2 - 75.2 (19.9)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.4"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     7   5
  2Q GAIN WILD-TYPE 199 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      7    5
  2Q GAIN WILD-TYPE  199  261
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               7               199
  MALE                 5               261
[1] 2 2
[1] FALSE
D4V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2Q GAIN MUTATED             6                2                 4
  2Q GAIN WILD-TYPE         170              116               174
D4V5, multiclass
                   clus
vv                  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASTROCYTOMA                     6               170
  OLIGOASTROCYTOMA                2               116
  OLIGODENDROGLIOMA               4               174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  10
  2Q GAIN WILD-TYPE  90 370
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   10
  2Q GAIN WILD-TYPE   90  370
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                2                90
  YES              10               370
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     0
  2Q GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           0    11
  2Q GAIN WILD-TYPE                        15   426
D4V7, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         11               426
[1] 4 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, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     1  10
  2Q GAIN WILD-TYPE  17 409
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   10
  2Q GAIN WILD-TYPE   17  409
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              10               409
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED     7   4
  3P GAIN WILD-TYPE 369  90
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               459 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                90 
$`3P GAIN MUTATED`
TCGA-CS-6668 TCGA-DU-6400 TCGA-DU-7013 TCGA-DU-8158 TCGA-E1-5304 TCGA-FG-5962 
        8.02         1.22         8.84         5.10        41.13        47.77 
TCGA-HT-7606 TCGA-HT-A4DS TCGA-P5-A5EZ TCGA-S9-A6WM TCGA-S9-A6WO 
       17.29         0.23         2.30        19.86        18.61 

$`3P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 
       23.84        17.95        12.43         8.48         7.56         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31        41.98         2.76        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       14.33         0.23         0.20        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       34.19        28.27        15.72        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP 
       80.12        32.45        84.99        31.10        15.91        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.23              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            47.77            211.17 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             8.84             18.77 
[1] "0.2 - 47.8 (8.8)"   "0.0 - 211.2 (18.8)"
[1] "hr=" "4"  
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     6   5
  3P GAIN WILD-TYPE 200 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    5
  3P GAIN WILD-TYPE  200  261
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               6               200
  MALE                 5               261
[1] 2 2
[1] FALSE
D5V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3P GAIN MUTATED             8                0                 3
  3P GAIN WILD-TYPE         168              118               175
D5V5, multiclass
                   clus
vv                  3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASTROCYTOMA                     8               168
  OLIGOASTROCYTOMA                0               118
  OLIGODENDROGLIOMA               3               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3   8
  3P GAIN WILD-TYPE  89 372
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    8
  3P GAIN WILD-TYPE   89  372
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                3                89
  YES               8               372
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           0    11
  3P GAIN WILD-TYPE                        15   426
D5V7, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         11               426
[1] 4 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, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  11
  3P GAIN WILD-TYPE  18 408
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   11
  3P GAIN WILD-TYPE   18  408
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              11               408
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED     4   4
  3Q GAIN WILD-TYPE 372  90
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               462 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                90 
$`3Q GAIN MUTATED`
TCGA-DU-6400 TCGA-DU-7013 TCGA-DU-8158 TCGA-E1-5304 TCGA-FG-5962 TCGA-HT-7606 
        1.22         8.84         5.10        41.13        47.77        17.29 
TCGA-HT-A4DS TCGA-S9-A6WM 
        0.23        19.86 

$`3Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       25.91        60.30        23.31        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       32.35        14.33         0.23         0.20        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        28.27        15.72        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.23              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            47.77            211.17 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           13.065            18.710 
[1] "0.2 - 47.8 (13.1)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "4.7"
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5   3
  3Q GAIN WILD-TYPE 201 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5    3
  3Q GAIN WILD-TYPE  201  263
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               5               201
  MALE                 3               263
[1] 2 2
[1] FALSE
D6V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3Q GAIN MUTATED             6                0                 2
  3Q GAIN WILD-TYPE         170              118               176
D6V5, multiclass
                   clus
vv                  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASTROCYTOMA                     6               170
  OLIGOASTROCYTOMA                0               118
  OLIGODENDROGLIOMA               2               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3   5
  3Q GAIN WILD-TYPE  89 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    5
  3Q GAIN WILD-TYPE   89  375
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                3                89
  YES               5               375
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  0     0
  3Q GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           0     8
  3Q GAIN WILD-TYPE                        15   429
D6V7, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          8               429
[1] 4 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, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     0   8
  3Q GAIN WILD-TYPE  18 411
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0    8
  3Q GAIN WILD-TYPE   18  411
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               8               411
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    11   0
  4P GAIN WILD-TYPE 365  94
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               459 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                94 
$`4P GAIN MUTATED`
TCGA-CS-4943 TCGA-CS-6665 TCGA-CS-6666 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-FG-A87Q 
       18.15        12.43         8.48        15.12         4.96         5.72 
TCGA-HT-7477 TCGA-HT-7857 TCGA-HT-A5R7 TCGA-S9-A6TU TCGA-S9-A7J0 
       24.26         0.23        20.22        87.12        20.02 

$`4P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       17.95         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
       81.96        75.25        47.93        72.92        50.86        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       46.72        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.17        14.24        12.59         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.03        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       39.09        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       28.27        15.72         0.23        26.04         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.14        16.83        21.40        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       62.17        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        7.13         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.23              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            87.12            211.17 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            15.12             18.71 
[1] "0.2 - 87.1 (15.1)"  "0.0 - 211.2 (18.7)"
[1] "hr="     "9200000"
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     5   6
  4P GAIN WILD-TYPE 201 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5    6
  4P GAIN WILD-TYPE  201  260
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               5               201
  MALE                 6               260
[1] 2 2
[1] FALSE
D7V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4P GAIN MUTATED             8                0                 3
  4P GAIN WILD-TYPE         168              118               175
D7V5, multiclass
                   clus
vv                  4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASTROCYTOMA                     8               168
  OLIGOASTROCYTOMA                0               118
  OLIGODENDROGLIOMA               3               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  10
  4P GAIN WILD-TYPE  91 370
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   10
  4P GAIN WILD-TYPE   91  370
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                91
  YES              10               370
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     0
  4P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1    10
  4P GAIN WILD-TYPE                        14   427
D7V7, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         10               427
[1] 4 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, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  10
  4P GAIN WILD-TYPE  18 409
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   10
  4P GAIN WILD-TYPE   18  409
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              10               409
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 372  93
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               465 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                93 
$`4Q GAIN MUTATED`
TCGA-DU-A5TT TCGA-HT-7477 TCGA-HT-7857 TCGA-HT-A5R7 TCGA-VW-A8FI 
        4.96        24.26         0.23        20.22         8.05 

$`4Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       15.12         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
       15.72         0.23        26.04         0.13         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.23              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            24.26            211.17 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             8.05             18.71 
[1] "0.2 - 24.3 (8.1)"   "0.0 - 211.2 (18.7)"
[1] "hr=" "3.1"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     2   3
  4Q GAIN WILD-TYPE 204 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    3
  4Q GAIN WILD-TYPE  204  263
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2               204
  MALE                 3               263
[1] 2 2
[1] FALSE
D8V4, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               267 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5395 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666        TCGA-CS-6667 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-DB-5274        TCGA-DB-A4XE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DB-A64L        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DB-A75L        TCGA-DB-A75O        TCGA-DH-5140        TCGA-DH-5142 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DH-5143        TCGA-DH-5144        TCGA-DH-A66B        TCGA-DH-A66D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7UU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DH-A7UV        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-5874        TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7011        TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7018        TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7299        TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7304        TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-8161        TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A5TS        TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A6S2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A6S6        TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A7T6        TCGA-DU-A7T8        TCGA-DU-A7TA        TCGA-DU-A7TB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A7TC        TCGA-DU-A7TD        TCGA-DU-A7TG        TCGA-E1-5302 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-5311        TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-A7YO        TCGA-E1-A7YV        TCGA-E1-A7YW        TCGA-E1-A7Z6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-5963        TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-8181        TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-A4MT        TCGA-FG-A4MW 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-A4MX        TCGA-FG-A60J        TCGA-FG-A60L        TCGA-FG-A6J1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-A6J3        TCGA-FG-A711        TCGA-FG-A713        TCGA-FG-A87Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7468        TCGA-HT-7470        TCGA-HT-7475        TCGA-HT-7485 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7607        TCGA-HT-7609        TCGA-HT-7611        TCGA-HT-7689 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7854 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7875        TCGA-HT-7884        TCGA-HT-8564        TCGA-HT-A4DV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-A5RA        TCGA-HT-A5RC        TCGA-HT-A615        TCGA-HT-A617 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-A618        TCGA-HT-A61B        TCGA-HT-A61C        TCGA-HT-A74L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IK-7675        TCGA-KT-A74X        TCGA-KT-A7W1        TCGA-P5-A5EU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX        TCGA-P5-A5F0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-P5-A5F2        TCGA-P5-A5F4        TCGA-P5-A5F6        TCGA-P5-A731 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A65R        TCGA-QH-A65S        TCGA-QH-A65V        TCGA-QH-A65X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A65Z        TCGA-QH-A6CS        TCGA-QH-A6CU        TCGA-QH-A6CV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A6CW        TCGA-QH-A6CX        TCGA-QH-A6CY        TCGA-QH-A6CZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A6X3        TCGA-QH-A6X4        TCGA-QH-A6X5        TCGA-QH-A6X8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A6X9        TCGA-QH-A6XA        TCGA-QH-A6XC        TCGA-QH-A86X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A870        TCGA-RY-A83Y        TCGA-RY-A840        TCGA-RY-A845 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-RY-A847        TCGA-S9-A6TS        TCGA-S9-A6TU        TCGA-S9-A6TV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6TW        TCGA-S9-A6TX        TCGA-S9-A6TY        TCGA-S9-A6TZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6U0        TCGA-S9-A6U1        TCGA-S9-A6U2        TCGA-S9-A6U5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6U6        TCGA-S9-A6U8        TCGA-S9-A6UA        TCGA-S9-A6UB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6WD        TCGA-S9-A6WE        TCGA-S9-A6WG        TCGA-S9-A6WH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6WI        TCGA-S9-A6WL        TCGA-S9-A6WM        TCGA-S9-A6WN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6WO        TCGA-S9-A6WP        TCGA-S9-A6WQ        TCGA-S9-A7IQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7IS        TCGA-S9-A7IX        TCGA-S9-A7IY        TCGA-S9-A7IZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7J0        TCGA-S9-A7J1        TCGA-S9-A7J2        TCGA-S9-A7J3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7QW        TCGA-S9-A7QX        TCGA-S9-A7QY        TCGA-S9-A7QZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7R1        TCGA-S9-A7R2        TCGA-S9-A7R3        TCGA-S9-A7R4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7R7        TCGA-S9-A7R8        TCGA-S9-A89V        TCGA-S9-A89Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A7C3        TCGA-TM-A7C4        TCGA-TM-A7C5        TCGA-TM-A7CA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A7CF        TCGA-TM-A84B        TCGA-TM-A84C        TCGA-TM-A84F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A84G        TCGA-TM-A84H        TCGA-TM-A84I        TCGA-TM-A84J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A84L        TCGA-TM-A84M        TCGA-TM-A84O        TCGA-TM-A84Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TM-A84T        TCGA-TQ-A7RW 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VM-A8C8        TCGA-VM-A8CA        TCGA-VM-A8CD        TCGA-VM-A8CE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VM-A8CH        TCGA-WY-A858        TCGA-WY-A859 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4Q GAIN MUTATED             4                0                 1
  4Q GAIN WILD-TYPE         172              118               177
D8V5, multiclass
                   clus
vv                  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASTROCYTOMA                     4               172
  OLIGOASTROCYTOMA                0               118
  OLIGODENDROGLIOMA               1               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   5
  4Q GAIN WILD-TYPE  92 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    5
  4Q GAIN WILD-TYPE   92  375
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                92
  YES               5               375
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     5
  4Q GAIN WILD-TYPE                        15   432
D8V7, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          5               432
[1] 4 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, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   5
  4Q GAIN WILD-TYPE  18 414
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    5
  4Q GAIN WILD-TYPE   18  414
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               5               414
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED     6   3
  5P GAIN WILD-TYPE 370  91
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9               461 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                91 
$`5P GAIN MUTATED`
TCGA-DU-A5TT TCGA-E1-5304 TCGA-HT-7477 TCGA-QH-A65S TCGA-QH-A6CV TCGA-S9-A6TS 
        4.96        41.13        24.26         2.53        14.53        62.17 
TCGA-TM-A7C3 TCGA-VM-A8C9 TCGA-VW-A8FI 
       49.45        30.08         8.05 

$`5P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       15.12         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.50        44.42         0.56        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.14        16.83        21.40        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65V 
       11.64         0.20         9.01        13.61        15.16        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX 
       15.85        14.04        19.33        14.83        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV 
       28.08         2.07        19.59        30.67        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        18.71        11.97        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             2.53              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            62.17            211.17 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            24.26             18.61 
[1] "2.5 - 62.2 (24.3)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.9"
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     4   5
  5P GAIN WILD-TYPE 202 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    5
  5P GAIN WILD-TYPE  202  261
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               4               202
  MALE                 5               261
[1] 2 2
[1] FALSE
D9V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5P GAIN MUTATED             6                2                 1
  5P GAIN WILD-TYPE         170              116               177
D9V5, multiclass
                   clus
vv                  5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASTROCYTOMA                     6               170
  OLIGOASTROCYTOMA                2               116
  OLIGODENDROGLIOMA               1               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1   8
  5P GAIN WILD-TYPE  91 372
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1    8
  5P GAIN WILD-TYPE   91  372
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                1                91
  YES               8               372
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     1
  5P GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           0     7
  5P GAIN WILD-TYPE                        15   430
D9V7, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          7               430
[1] 4 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, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     0   8
  5P GAIN WILD-TYPE  18 411
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0    8
  5P GAIN WILD-TYPE   18  411
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               8               411
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     5   1
  5Q GAIN WILD-TYPE 371  93
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               464 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                93 
$`5Q GAIN MUTATED`
TCGA-DU-A5TT TCGA-QH-A65S TCGA-QH-A6CV TCGA-TM-A7C3 TCGA-VM-A8C9 TCGA-VW-A8FI 
        4.96         2.53        14.53        49.45        30.08         8.05 

$`5Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       15.12         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
       15.16        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       15.98        26.99        43.04        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       35.93        23.47        37.05        16.01        23.21        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2.53              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            49.45            211.17 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            11.29             18.71 
[1] "2.5 - 49.5 (11.3)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "1.5"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3   3
  5Q GAIN WILD-TYPE 203 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    3
  5Q GAIN WILD-TYPE  203  263
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               3               203
  MALE                 3               263
[1] 2 2
[1] FALSE
D10V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5Q GAIN MUTATED             3                2                 1
  5Q GAIN WILD-TYPE         173              116               177
D10V5, multiclass
                   clus
vv                  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASTROCYTOMA                     3               173
  OLIGOASTROCYTOMA                2               116
  OLIGODENDROGLIOMA               1               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0   6
  5Q GAIN WILD-TYPE  92 374
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    6
  5Q GAIN WILD-TYPE   92  374
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                92
  YES               6               374
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           0     4
  5Q GAIN WILD-TYPE                        15   433
D10V7, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          4               433
[1] 4 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, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0   5
  5Q GAIN WILD-TYPE  18 414
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    5
  5Q GAIN WILD-TYPE   18  414
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               5               414
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     6   1
  6P GAIN WILD-TYPE 370  93
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               463 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                93 
$`6P GAIN MUTATED`
TCGA-CS-6665 TCGA-DU-6408 TCGA-DU-6542 TCGA-FG-A6J3 TCGA-HT-7606 TCGA-HT-8563 
       12.43       114.08         7.73        22.26        17.29        28.27 
TCGA-P5-A5EZ 
        2.30 

$`6P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 
      133.74        19.89        16.83        94.52         7.96        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        0.23        29.59        34.19        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             2.30              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           114.08            211.17 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            17.29             18.71 
[1] "2.3 - 114.1 (17.3)" "0.0 - 211.2 (18.7)"
[1] "hr=" "1.5"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5   2
  6P GAIN WILD-TYPE 201 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    2
  6P GAIN WILD-TYPE  201  264
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5               201
  MALE                 2               264
[1] 2 2
[1] FALSE
D11V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6P GAIN MUTATED             5                1                 1
  6P GAIN WILD-TYPE         171              117               177
D11V5, multiclass
                   clus
vv                  6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASTROCYTOMA                     5               171
  OLIGOASTROCYTOMA                1               117
  OLIGODENDROGLIOMA               1               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2   5
  6P GAIN WILD-TYPE  90 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    5
  6P GAIN WILD-TYPE   90  375
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                2                90
  YES               5               375
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     0
  6P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           0     7
  6P GAIN WILD-TYPE                        15   430
D11V7, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          7               430
[1] 4 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, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0   7
  6P GAIN WILD-TYPE  18 412
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    7
  6P GAIN WILD-TYPE   18  412
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               7               412
[1] 2 2
[1] FALSE

Clustering(12) Variable = 7P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    73  37
  7P GAIN WILD-TYPE 303  57
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              110               360 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               37                57 
$`7P GAIN MUTATED`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
        7.69        43.89        40.18        21.01         9.96         6.38 
TCGA-CS-6186 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 TCGA-DB-A4X9 
       17.69        12.43         6.61       122.73        50.86        46.42 
TCGA-DB-A4XE TCGA-DB-A64O TCGA-DB-A75O TCGA-DH-A669 TCGA-DH-A66G TCGA-DH-A7UT 
       37.45        25.48        30.74        30.21        17.19        13.38 
TCGA-DH-A7UV TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6400 TCGA-DU-6402 
       18.61         8.45       211.17        49.02         1.22         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 
       11.64       133.74        19.89        16.83        94.52         7.96 
TCGA-DU-7006 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       11.47       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT 
       23.74        20.68        19.13        16.96        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R 
        3.65         5.65        12.20        11.41        26.76        21.30 
TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-5962 
       77.88         7.50         0.56        41.13       130.78        47.77 
TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 
       18.77        23.97        18.44        15.35        20.09        13.68 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7473 TCGA-HT-7477 
       10.72        18.38        10.78         5.72        16.54        24.26 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 
        0.49         3.72        11.28        16.24        63.55        12.23 
TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RC 
       13.78        15.72         0.23         0.13         0.07         5.33 
TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.14        21.40        17.65         2.43        10.52        15.35 
TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-P5-A72U TCGA-P5-A731 TCGA-QH-A6CS TCGA-QH-A6CV 
       14.40         4.11         0.16         9.01        19.33        14.53 
TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-RY-A845 TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM 
        1.91         5.03        19.59        31.33        22.95        19.86 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7R2 
       36.13        22.32         7.13        20.02        15.06        10.39 
TCGA-TM-A7C3 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84M TCGA-TQ-A7RH 
       49.45        34.78        24.92        30.44        24.79        15.98 
TCGA-VW-A8FI TCGA-WY-A85E 
        8.05        20.81 

$`7P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-6188 
        4.70        18.15        10.62        64.64         0.10        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 
       17.95         8.48         7.56         8.02         7.40        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        50.17        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF 
       78.28        18.84        30.21        46.72        39.78        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        31.63        24.20        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       11.24        17.88        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR 
       14.40         8.02        42.05        27.81        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.12         3.45        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
       13.38         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       52.11        22.42        75.16        46.06        65.75        87.45 
TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
      114.08         7.73        62.96       156.23       138.28        14.99 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 
        2.76         5.10        14.60        21.40        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       14.24        15.12         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC 
        5.98         7.13        17.98       124.50        42.31        23.51 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       78.21        95.57        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       14.33         0.23         0.20        25.48        34.36        36.82 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 
       14.93        24.99        17.88        22.55        20.61        12.95 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       38.27        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        22.26        28.54        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       20.45        13.58        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       40.11         0.13         0.03         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 
       19.23        39.09         0.23        50.63        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 
        0.33         0.13         3.68         5.33        35.47        31.43 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
        1.64         9.40         0.10        37.87        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 
        0.10         0.46         2.50         5.56         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB 
       34.19        28.27        26.04        20.22        27.35         0.10 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74L 
        2.70        16.93         1.81        16.83        17.52        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X 
        5.88         7.63         0.76         1.28        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
       11.64         0.20        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       15.85        14.04        14.83        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA 
        9.17        10.29        14.53        16.34        16.73        16.50 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 
       30.87         5.46         9.90        28.08         2.07        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ 
       62.17        87.12        18.77        37.84        34.49        28.70 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        15.91        18.61        15.16        14.07 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX 
        7.92        23.51         8.19         2.04        17.03        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       28.37        13.02       169.84        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF 
       31.59        18.71        11.97        48.33        49.32        48.39 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        40.64        28.08        24.16        40.83 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RW 
       33.24        25.38        18.61        14.93        23.80        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K 
       23.47        37.05        16.01        23.21        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           211.17            182.33 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           16.685            19.230 
[1] "0.1 - 211.2 (16.7)" "0.0 - 182.3 (19.2)"
[1] "hr=" "2.5"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    54  56
  7P GAIN WILD-TYPE 152 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     54   56
  7P GAIN WILD-TYPE  152  210
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              54               152
  MALE                56               210
[1] 2 2
[1] FALSE
D12V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7P GAIN MUTATED            47               29                34
  7P GAIN WILD-TYPE         129               89               144
D12V5, multiclass
                   clus
vv                  7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASTROCYTOMA                    47               129
  OLIGOASTROCYTOMA               29                89
  OLIGODENDROGLIOMA              34               144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    23  87
  7P GAIN WILD-TYPE  69 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     23   87
  7P GAIN WILD-TYPE   69  293
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               23                69
  YES              87               293
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     2
  7P GAIN WILD-TYPE                                0     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           7    99
  7P GAIN WILD-TYPE                         8   338
D12V7, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 6
  BLACK OR AFRICAN AMERICAN                      7                 8
  WHITE                                         99               338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     5 100
  7P GAIN WILD-TYPE  13 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5  100
  7P GAIN WILD-TYPE   13  319
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                13
  NOT HISPANIC OR LATINO             100               319
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    98  43
  7Q GAIN WILD-TYPE 278  51
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              141               329 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               43                51 
$`7Q GAIN MUTATED`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
        7.69        43.89        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 TCGA-DB-A4X9 
       23.84        12.43         6.61       122.73        50.86        46.42 
TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DB-A64O TCGA-DB-A64X TCGA-DB-A75O TCGA-DH-A669 
       30.21        37.45        25.48        18.51        30.74        30.21 
TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5854 TCGA-DU-6392 
       17.19        13.38        18.61        14.56         8.45       211.17 
TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       49.02        65.75         1.22         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7011 
       19.89        16.83        94.52         7.96        11.47       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7292 TCGA-DU-7301 TCGA-DU-7306 
        6.54         8.84       117.40         7.96        25.91        41.98 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT 
       23.74        20.68        19.13        16.96        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L 
        3.65         5.65        12.20        77.98        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5302 
       21.30       124.50        77.88         7.50         0.56        50.14 
TCGA-E1-5304 TCGA-E1-5322 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5965 TCGA-FG-6688 
       41.13       130.78         0.20        47.77        36.82        18.77 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 
       24.99        23.97        18.44        15.35        20.09        13.68 
TCGA-FG-8186 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7473 
       16.01        10.72        18.38        10.78         5.72        16.54 
TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7610 TCGA-HT-7693 TCGA-HT-7860 
       17.42        24.26       122.47        56.09        17.52         0.49 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8108 
        3.72        11.28        16.24        63.55        12.23         2.50 
TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
       13.78        15.72         0.23         0.13         0.07        27.35 
TCGA-HT-A5RC TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H 
        5.33         1.81        16.14        21.40        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ 
       10.52        15.35         0.10         4.31        17.82        20.35 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A72U TCGA-P5-A731 
       14.40         0.23         2.30         4.11         0.16         9.01 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XA TCGA-QH-A6XC 
       19.33        14.83        14.53        12.23        16.50         5.03 
TCGA-RY-A845 TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A7IQ 
       19.59        31.33        22.95        19.86        18.61        36.13 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7R2 
       22.32         7.13        20.02        15.06        28.37        10.39 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84M 
       49.45        48.33        34.78        24.92        30.44        24.79 
TCGA-TQ-A7RH TCGA-VW-A8FI TCGA-WY-A85E 
       15.98         8.05        20.81 

$`7Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 
        4.70        18.15        10.62        64.64        40.18         0.10 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 
       17.95         8.48         7.56         8.02         7.40        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        50.17        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       78.28        18.84        46.72        39.78        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       31.63        24.20        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       27.81        29.23        14.40        12.10        11.24        17.88 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       16.18        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU 
       42.05        27.81        17.19        54.25        13.12         3.45 
TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 
       18.02        17.46         6.74        13.38         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 
       18.94        17.49        15.16        52.11        22.42        75.16 
TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 
       46.06        87.45       114.08         7.73        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
      138.28        14.99        90.77        30.67        26.30        10.36 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        44.02        62.01        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 
        2.76         5.10        14.60        21.40        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 
       14.24        15.12         8.65         2.70         7.23         5.98 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5303 
        7.13        17.98        42.31        23.51        44.42        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO 
       79.99        57.93       134.27        78.21        95.57        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5963 
       32.45        36.82        32.35        14.33         0.23        25.48 
TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 
       34.36        14.93        17.88        22.55        20.61        12.95 
TCGA-FG-8185 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        22.26        28.54        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       13.58        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
        0.13         0.03         3.75         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       29.85        23.18         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       45.99        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         0.10         2.96         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 
       39.48        19.23        39.09         0.23        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       31.43         1.64         9.40         0.10        37.87        33.01 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 
        6.25         0.10         0.46         5.56         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 
       34.19        28.27        26.04        20.22         0.10         2.70 
TCGA-HT-A615 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 
       16.93        16.83        17.52        11.05        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18        35.90        21.70        21.60 
TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       19.59        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F1 TCGA-P5-A5F2 
       14.40         6.71         1.64         2.37         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        0.76         1.28        10.42        13.25        11.64         0.20 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       13.61         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.73         1.91        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
        2.07        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       34.49        28.70        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP 
       80.12        32.45        84.99        31.10        15.91        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       14.07         7.92        23.51         8.19         2.04        17.03 
TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.12        13.02       169.84        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C 
       31.59        18.71        11.97        49.32        48.39        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O 
       59.05        40.64        28.08        24.16        40.83        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RW TCGA-VM-A8C8 
       25.38        18.61        14.93        23.80        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       37.05        16.01        23.21        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       39.88        43.40        45.80        46.88        37.71 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           211.17            182.33 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            17.42             19.59 
[1] "0.1 - 211.2 (17.4)" "0.0 - 182.3 (19.6)"
[1] "hr=" "2.3"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    66  75
  7Q GAIN WILD-TYPE 140 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     66   75
  7Q GAIN WILD-TYPE  140  191
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              66               140
  MALE                75               191
[1] 2 2
[1] FALSE
D13V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7Q GAIN MUTATED            61               38                42
  7Q GAIN WILD-TYPE         115               80               136
D13V5, multiclass
                   clus
vv                  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASTROCYTOMA                    61               115
  OLIGOASTROCYTOMA               38                80
  OLIGODENDROGLIOMA              42               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"
D13V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    31 110
  7Q GAIN WILD-TYPE  61 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     31  110
  7Q GAIN WILD-TYPE   61  270
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               31                61
  YES             110               270
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  1     3
  7Q GAIN WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           8   128
  7Q GAIN WILD-TYPE                         7   309
D13V7, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 5
  BLACK OR AFRICAN AMERICAN                      8                 7
  WHITE                                        128               309
[1] 4 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, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     6 130
  7Q GAIN WILD-TYPE  12 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6  130
  7Q GAIN WILD-TYPE   12  289
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                12
  NOT HISPANIC OR LATINO             130               289
[1] 2 2
[1] FALSE

Clustering(14) Variable = 8P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    34   9
  8P GAIN WILD-TYPE 342  85
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               43               427 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9                85 
$`8P GAIN MUTATED`
TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5281 TCGA-DB-A64X TCGA-DH-A669 TCGA-DH-A7UT 
       12.43         8.48        78.28        18.51        30.21        13.38 
TCGA-DU-5871 TCGA-DU-6407 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7304 TCGA-DU-8158 
       18.94        94.52         8.84       117.40        23.31         5.10 
TCGA-DU-8163 TCGA-DU-A5TS TCGA-DU-A6S7 TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-E1-5303 
       20.68        15.12         7.23        17.98        77.88        67.46 
TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A4MT TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 
       47.77        15.35        38.27         6.54        24.26        40.34 
TCGA-HT-7482 TCGA-HT-7855 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8106 TCGA-HT-8111 
      106.95        19.23        16.24        63.55         0.10         0.23 
TCGA-HT-A5R7 TCGA-HT-A74J TCGA-S9-A6TY TCGA-S9-A6WH TCGA-S9-A6WO TCGA-S9-A7QX 
       20.22        10.52        31.33        32.45        18.61        13.12 
TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84Q TCGA-TQ-A7RH TCGA-VM-A8C8 
       11.97        48.39        30.44        25.38        15.98        43.04 
TCGA-VM-A8CA 
       13.51 

$`8P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       46.72        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       27.81        29.23        14.40        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       30.74        16.18        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
        8.02        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.12         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
      133.74        19.89        16.83       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        6.54        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8165 
       41.98         2.76        23.74        14.60        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT 
       16.96        15.48        14.17        14.24        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 
       14.93        24.99        23.97        18.44        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        14.96        22.52        32.61        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 
       17.42         6.38        75.19        95.93       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        2.96        17.52         6.90        14.53        39.48        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       31.43         1.64         9.40         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         6.25         0.46         2.50         5.56        13.78 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
       17.65         2.43        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP 
       80.12        84.99        31.10        19.86        15.91        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY 
       20.02         8.19         2.04        17.03        15.06        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        18.71        49.45        48.33        49.32        34.78 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       24.92        16.18        59.05        40.64        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        24.79        33.24        18.61        14.93        23.80 
TCGA-TQ-A7RW TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       26.99        30.08         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.10              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           117.40            211.17 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            19.23             18.61 
[1] "0.1 - 117.4 (19.2)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    16  27
  8P GAIN WILD-TYPE 190 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     16   27
  8P GAIN WILD-TYPE  190  239
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              16               190
  MALE                27               239
[1] 2 2
[1] FALSE
D14V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8P GAIN MUTATED            20               11                12
  8P GAIN WILD-TYPE         156              107               166
D14V5, multiclass
                   clus
vv                  8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASTROCYTOMA                    20               156
  OLIGOASTROCYTOMA               11               107
  OLIGODENDROGLIOMA              12               166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     7  36
  8P GAIN WILD-TYPE  85 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      7   36
  8P GAIN WILD-TYPE   85  344
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                7                85
  YES              36               344
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     0
  8P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           1    40
  8P GAIN WILD-TYPE                        14   397
D14V7, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         40               397
[1] 4 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, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2  39
  8P GAIN WILD-TYPE  16 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   39
  8P GAIN WILD-TYPE   16  380
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                16
  NOT HISPANIC OR LATINO              39               380
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    40  11
  8Q GAIN WILD-TYPE 336  83
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               51               419 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               11                83 
$`8Q GAIN MUTATED`
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A64X 
       17.95        12.43         8.48        50.86        78.28        18.51 
TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A7UT TCGA-DU-5871 TCGA-DU-6407 TCGA-DU-7013 
       14.40        30.21        13.38        18.94        94.52         8.84 
TCGA-DU-7014 TCGA-DU-7304 TCGA-DU-8158 TCGA-DU-8163 TCGA-DU-A5TS TCGA-DU-A5TW 
      117.40        23.31         5.10        20.68        15.12         5.65 
TCGA-DU-A6S7 TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-E1-5303 TCGA-FG-5962 TCGA-FG-6691 
        7.23        17.98        77.88        67.46        47.77        23.97 
TCGA-FG-7634 TCGA-FG-A4MT TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7482 
       15.35        38.27         6.54        24.26        40.34       106.95 
TCGA-HT-7855 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-A5R7 
       19.23        16.24        63.55         0.10         0.23        20.22 
TCGA-HT-A74J TCGA-P5-A5F1 TCGA-S9-A6TY TCGA-S9-A6WH TCGA-S9-A6WO TCGA-S9-A7QW 
       10.52         5.88        31.33        32.45        18.61        15.06 
TCGA-S9-A7QX TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84Q TCGA-TQ-A7RH 
       13.12        11.97        48.39        30.44        25.38        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CA 
       26.99        43.04        13.51 

$`8Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       23.84         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        46.42        18.84        30.21        46.72        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       37.45        33.57        72.95        31.63        24.20        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       14.40        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       19.96        31.82        30.31         8.02        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        54.25        13.12         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7015 TCGA-DU-7018 
      138.28        14.99       105.21         6.54        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       62.01        25.91        60.30        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       14.60        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 
       14.24        12.59         4.96         3.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
        2.70        77.98         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
       21.30       124.50        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        50.14        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       32.35        14.33         0.23         0.20        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 
       36.82        18.77        14.93        24.99        18.44        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU 
       16.01        20.09        14.96        22.52        32.61        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 
        3.75        17.42         6.38        75.19        95.93       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 
       11.28        31.43         1.64         9.40         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         6.25         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       13.78        29.59        34.19        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04         0.13         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.52        17.65         2.43        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP 
       80.12        84.99        31.10        19.86        15.91        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ 
       20.02         8.19         2.04        17.03        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B 
       18.71        49.45        48.33        49.32        34.78        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        40.64        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 
       24.79        33.24        18.61        14.93        23.80        30.08 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           117.40            211.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            18.94             18.61 
[1] "0.1 - 117.4 (18.9)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1.1"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    19  32
  8Q GAIN WILD-TYPE 187 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     19   32
  8Q GAIN WILD-TYPE  187  234
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              19               187
  MALE                32               234
[1] 2 2
[1] FALSE
D15V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8Q GAIN MUTATED            26               12                13
  8Q GAIN WILD-TYPE         150              106               165
D15V5, multiclass
                   clus
vv                  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASTROCYTOMA                    26               150
  OLIGOASTROCYTOMA               12               106
  OLIGODENDROGLIOMA              13               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    10  41
  8Q GAIN WILD-TYPE  82 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     10   41
  8Q GAIN WILD-TYPE   82  339
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               10                82
  YES              41               339
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     0
  8Q GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           2    46
  8Q GAIN WILD-TYPE                        13   391
D15V7, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      2                13
  WHITE                                         46               391
[1] 4 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, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3  45
  8Q GAIN WILD-TYPE  15 374
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3   45
  8Q GAIN WILD-TYPE   15  374
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              45               374
[1] 2 2
[1] FALSE

Clustering(16) Variable = 9P GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    11   4
  9P GAIN WILD-TYPE 365  90
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               455 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4                90 
$`9P GAIN MUTATED`
TCGA-CS-5396 TCGA-CS-6665 TCGA-DB-A4XE TCGA-DU-7010 TCGA-DU-8158 TCGA-DU-8161 
        9.96        12.43        37.45        14.99         5.10        23.74 
TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A76O TCGA-E1-5302 TCGA-HT-7474 TCGA-HT-A61B 
       19.13         4.96         7.13        50.14         3.75        17.52 
TCGA-S9-A6WH TCGA-S9-A6WM TCGA-TM-A7C4 
       32.45        19.86        48.33 

$`9P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       30.21        46.72        39.78        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       23.31        41.98         2.76        14.60        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 
        7.23         5.98        11.41        26.76        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 
       40.11         0.13         0.03        16.54        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59        34.19        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       21.40        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL 
      106.39        69.50        72.59        80.12        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       11.97        49.45        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             3.75              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            50.14            211.17 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            17.52             18.71 
[1] "3.8 - 50.1 (17.5)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "2.2"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    10   5
  9P GAIN WILD-TYPE 196 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     10    5
  9P GAIN WILD-TYPE  196  261
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              10               196
  MALE                 5               261
[1] 2 2
[1] FALSE
D16V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9P GAIN MUTATED             8                4                 3
  9P GAIN WILD-TYPE         168              114               175
D16V5, multiclass
                   clus
vv                  9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASTROCYTOMA                     8               168
  OLIGOASTROCYTOMA                4               114
  OLIGODENDROGLIOMA               3               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3  12
  9P GAIN WILD-TYPE  89 368
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3   12
  9P GAIN WILD-TYPE   89  368
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                3                89
  YES              12               368
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0    15
  9P GAIN WILD-TYPE                        15   422
D16V7, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         15               422
[1] 4 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, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  15
  9P GAIN WILD-TYPE  18 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   15
  9P GAIN WILD-TYPE   18  404
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              15               404
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9Q GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    17   5
  9Q GAIN WILD-TYPE 359  89
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               22               448 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5                89 
$`9Q GAIN MUTATED`
TCGA-CS-5396 TCGA-CS-6665 TCGA-DB-A4XE TCGA-DU-7010 TCGA-DU-7298 TCGA-DU-8158 
        9.96        12.43        37.45        14.99        18.94         5.10 
TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A76O TCGA-E1-5302 TCGA-FG-A4MY 
       23.74        19.13         4.96         7.13        50.14        23.70 
TCGA-FG-A6J3 TCGA-FG-A87N TCGA-HT-7477 TCGA-HT-A61B TCGA-HW-8319 TCGA-S9-A6TW 
       22.26        13.58        24.26        17.52        21.70        37.84 
TCGA-S9-A6WH TCGA-S9-A6WM TCGA-S9-A7QW TCGA-WY-A85E 
       32.45        19.86        15.06        20.81 

$`9Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       30.21        46.72        39.78        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
       41.98         2.76        14.60        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
        5.98        11.41        26.76        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J 
       32.61        38.27        10.72        18.38        18.71        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       36.66        48.69        20.45         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.14        16.83        21.40        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18        35.90         4.31        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL 
      106.39        69.50        72.59        80.12        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       17.03        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.40        45.80        46.88        37.71 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             4.96              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            50.14            211.17 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           19.495            18.610 
[1] "5.0 - 50.1 (19.5)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.9"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    16   6
  9Q GAIN WILD-TYPE 190 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     16    6
  9Q GAIN WILD-TYPE  190  260
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              16               190
  MALE                 6               260
[1] 2 2
[1] FALSE
D17V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9Q GAIN MUTATED            13                5                 4
  9Q GAIN WILD-TYPE         163              113               174
D17V5, multiclass
                   clus
vv                  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASTROCYTOMA                    13               163
  OLIGOASTROCYTOMA                5               113
  OLIGODENDROGLIOMA               4               174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3  19
  9Q GAIN WILD-TYPE  89 361
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3   19
  9Q GAIN WILD-TYPE   89  361
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                3                89
  YES              19               361
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     1
  9Q GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1    20
  9Q GAIN WILD-TYPE                        14   417
D17V7, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         20               417
[1] 4 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, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  20
  9Q GAIN WILD-TYPE  17 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   20
  9Q GAIN WILD-TYPE   17  399
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              20               399
[1] 2 2
[1] FALSE

Clustering(18) Variable = 10P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    42  11
  10P GAIN WILD-TYPE 334  83
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                53                417 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                11                 83 
$`10P GAIN MUTATED`
TCGA-CS-5393 TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5277 TCGA-DB-A75M TCGA-DH-A66B 
       40.18        12.43         7.56        50.86        17.88        42.05 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-6396 TCGA-DU-7014 TCGA-DU-7019 TCGA-DU-7299 
        3.45        18.61        75.16       117.40        26.30        44.02 
TCGA-DU-7304 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YW 
       23.31        12.59        15.12        41.13       130.78        36.82 
TCGA-FG-A4MY TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A87N TCGA-HT-7470 TCGA-HT-7473 
       23.70        16.41        28.54        13.58        40.11        16.54 
TCGA-HT-7476 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7688 TCGA-HT-7879 
        6.54        40.34       106.95       172.77        31.69         3.68 
TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-A74O TCGA-HW-7493 TCGA-IK-7675 
        0.10         0.23        34.19         0.10        35.90        19.00 
TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72X TCGA-QH-A6XA TCGA-RY-A83Z TCGA-S9-A7IS 
        2.30         5.88        13.25        16.50         9.90         7.92 
TCGA-S9-A7J0 TCGA-S9-A89Z TCGA-TM-A7CA TCGA-TM-A84H TCGA-TQ-A7RH TCGA-VM-A8C8 
       20.02        11.97        34.78        30.44        15.98        43.04 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85E 
       13.32        43.96        39.88        43.40        20.81 

$`10P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       17.95         8.48         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       39.78        37.45        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75O 
       29.23        14.40        18.51        12.10        11.24        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       16.18        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       13.38        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 
      211.17        52.11        22.42        49.02        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84        90.77        30.67        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 
       18.94        62.01        25.91        60.30        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TU 
       16.96        15.48        14.17        14.24         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-EZ-7264 
       78.21        95.57        75.02        32.45        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K 
       38.27        10.72        18.38        18.71        14.76        17.82 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        22.26        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       20.45         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 
        0.13         0.03         3.75        17.42        24.26         6.38 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       75.19        95.93         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 
       23.61        37.15         0.33         0.13         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8563 
        0.46         2.50         5.56        13.78        29.59        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.14        16.83        21.40        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       10.52        15.35        11.05        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        20.35        12.76        20.81        20.71        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34        16.73         1.91         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 
       14.07        36.13        22.32        23.51         7.13         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84B 
       18.71        49.45        48.33        49.32        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        40.64        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RW TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       26.99        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       45.80        46.88        37.71 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.10               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            172.77             211.17 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             20.81              18.51 
[1] "0.1 - 172.8 (20.8)" "0.0 - 211.2 (18.5)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    19  34
  10P GAIN WILD-TYPE 187 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     19   34
  10P GAIN WILD-TYPE  187  232
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               19                187
  MALE                 34                232
[1] 2 2
[1] FALSE
D18V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10P GAIN MUTATED            28               17                 8
  10P GAIN WILD-TYPE         148              101               170
D18V5, multiclass
                   clus
vv                  10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASTROCYTOMA                     28                148
  OLIGOASTROCYTOMA                17                101
  OLIGODENDROGLIOMA                8                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    17  36
  10P GAIN WILD-TYPE  75 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     17   36
  10P GAIN WILD-TYPE   75  344
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                17                 75
  YES               36                344
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     1
  10P GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           1    50
  10P GAIN WILD-TYPE                        14   387
D18V7, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          50                387
[1] 4 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, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     5  42
  10P GAIN WILD-TYPE  13 377
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5   42
  10P GAIN WILD-TYPE   13  377
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 13
  NOT HISPANIC OR LATINO               42                377
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     8   1
  10Q GAIN WILD-TYPE 368  93
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 9                461 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 93 
$`10Q GAIN MUTATED`
TCGA-CS-5393 TCGA-DB-5277 TCGA-DU-A5TS TCGA-FG-A87N TCGA-HT-7476 TCGA-HT-8106 
       40.18        50.86        15.12        13.58         6.54         0.10 
TCGA-RY-A83Z TCGA-S9-A7J0 TCGA-S9-A89Z 
        9.90        20.02        11.97 

$`10Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       20.45         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 
       32.65        59.38        30.87         5.46        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        22.32        23.51         7.13         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.10               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             50.86             211.17 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             13.58              18.71 
[1] "0.1 - 50.9 (13.6)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "1.1"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   6
  10Q GAIN WILD-TYPE 203 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    6
  10Q GAIN WILD-TYPE  203  260
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                3                203
  MALE                  6                260
[1] 2 2
[1] FALSE
D19V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10Q GAIN MUTATED             7                0                 2
  10Q GAIN WILD-TYPE         169              118               176
D19V5, multiclass
                   clus
vv                  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASTROCYTOMA                      7                169
  OLIGOASTROCYTOMA                 0                118
  OLIGODENDROGLIOMA                2                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   6
  10Q GAIN WILD-TYPE  89 374
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    6
  10Q GAIN WILD-TYPE   89  374
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 3                 89
  YES                6                374
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     1
  10Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           1     7
  10Q GAIN WILD-TYPE                        14   430
D19V7, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                           7                430
[1] 4 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, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   7
  10Q GAIN WILD-TYPE  17 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    7
  10Q GAIN WILD-TYPE   17  412
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO                7                412
[1] 2 2
[1] FALSE

Clustering(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    26   4
  11P GAIN WILD-TYPE 350  90
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                30                440 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 90 
$`11P GAIN MUTATED`
TCGA-CS-5396 TCGA-CS-6666 TCGA-DB-A4X9 TCGA-DB-A64L TCGA-DH-5144 TCGA-DH-A66D 
        9.96         8.48        46.42        24.20         8.02        27.81 
TCGA-DU-5871 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-7018 TCGA-DU-7306 
       18.94       211.17        52.11         1.22        30.67        41.98 
TCGA-DU-8168 TCGA-DU-A5TW TCGA-DU-A6S8 TCGA-FG-5962 TCGA-FG-7634 TCGA-HT-7474 
       14.17         5.65         5.98        47.77        15.35         3.75 
TCGA-HT-7684 TCGA-HT-8109 TCGA-HT-A74K TCGA-QH-A65X TCGA-QH-A6CZ TCGA-RY-A845 
        6.05         5.56        15.35        15.85         9.17        19.59 
TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6WH TCGA-S9-A7QY TCGA-TQ-A7RW TCGA-VM-A8CA 
       37.84        31.33        32.45        28.37        26.99        13.51 

$`11P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        78.28        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       46.72        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       30.74        16.18        19.96        31.82        30.31        14.40 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        42.05        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       15.16        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
      117.40        90.77        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       19.13        16.96        15.48        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         3.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        7.23        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
       36.82        32.35        14.33         0.23         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       18.44        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.13         0.03        16.54        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        2.43        10.52        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       12.62        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       12.23         2.20        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       28.08         2.07        30.67        62.17        87.12        18.77 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       34.49        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        13.12        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       15.98        43.04        30.08         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.22               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            211.17             182.33 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            17.395             18.660 
[1] "1.2 - 211.2 (17.4)" "0.0 - 182.3 (18.7)"
[1] "hr=" "1.4"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    17  13
  11P GAIN WILD-TYPE 189 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     17   13
  11P GAIN WILD-TYPE  189  253
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               17                189
  MALE                 13                253
[1] 2 2
[1] FALSE
D20V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11P GAIN MUTATED             4               10                16
  11P GAIN WILD-TYPE         172              108               162
D20V5, multiclass
                   clus
vv                  11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASTROCYTOMA                      4                172
  OLIGOASTROCYTOMA                10                108
  OLIGODENDROGLIOMA               16                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6  24
  11P GAIN WILD-TYPE  86 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6   24
  11P GAIN WILD-TYPE   86  356
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 6                 86
  YES               24                356
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           1    28
  11P GAIN WILD-TYPE                        14   409
D20V7, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          28                409
[1] 4 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, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  27
  11P GAIN WILD-TYPE  16 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   27
  11P GAIN WILD-TYPE   16  392
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               27                392
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    48   8
  11Q GAIN WILD-TYPE 328  86
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                56                414 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                 86 
$`11Q GAIN MUTATED`
TCGA-CS-5396 TCGA-DB-5277 TCGA-DB-A4X9 TCGA-DB-A64L TCGA-DB-A64Q TCGA-DB-A75L 
        9.96        50.86        46.42        24.20         5.98        11.24 
TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT TCGA-DU-5870 TCGA-DU-5871 
        8.02        27.81        17.19        13.38       182.33        18.94 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-7018 TCGA-DU-7304 
      211.17        52.11        46.06         1.22        30.67        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A6S8 TCGA-FG-5962 
       41.98         2.76         4.96         5.65         5.98        47.77 
TCGA-FG-7634 TCGA-FG-A60L TCGA-HT-7474 TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7607 
       15.35        16.41         3.75         5.03       122.47         3.16 
TCGA-HT-7684 TCGA-HT-7688 TCGA-HT-7693 TCGA-HT-8109 TCGA-HT-A74K TCGA-HW-7490 
        6.05        31.69        17.52         5.56        15.35        19.23 
TCGA-HW-8319 TCGA-P5-A72W TCGA-QH-A65S TCGA-QH-A65X TCGA-QH-A6CZ TCGA-RY-A840 
       21.70        10.42         2.53        15.85         9.17        28.08 
TCGA-RY-A845 TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A7IZ 
       19.59        37.84        31.33        69.50        32.45         7.13 
TCGA-S9-A7QY TCGA-S9-A89Z TCGA-TM-A84J TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CA 
       28.37        11.97        24.16        26.99        43.04        13.51 
TCGA-WY-A85B TCGA-WY-A85C 
       45.80        46.88 

$`11Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        78.28        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       46.72        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       25.48        30.12        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       14.40        18.51        12.10        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40        30.21        42.05 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       17.19        54.25        13.12         3.45        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
       17.49        15.16        22.42        49.02        75.16        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
      117.40        90.77        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-8158 
       18.94        44.02        62.01        25.91        60.30         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K 
       12.20         8.65         2.70        77.98         7.23        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       14.33         0.23         0.20        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        24.99        23.97        18.44        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 
       95.93       106.95       172.77         4.01        29.85        23.18 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57        17.29        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 
       11.05         0.10        29.92        19.89         8.32        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.90         4.31        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       12.62        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       12.23         2.20        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX 
        2.07        30.67        62.17        87.12        18.77        34.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93         5.85       106.39        72.59        80.12 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
       14.07        36.13         7.92        22.32        23.51        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ 
        8.19         2.04        17.03        15.06        13.12        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       18.71        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       23.80        15.98        30.08         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85D TCGA-WY-A85E 
       13.32        43.96        39.88        43.40        37.71        20.81 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.22               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            211.17             172.77 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            19.085             18.610 
[1] "1.2 - 211.2 (19.1)" "0.0 - 172.8 (18.6)"
[1] "hr=" "1.6"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    29  27
  11Q GAIN WILD-TYPE 177 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     29   27
  11Q GAIN WILD-TYPE  177  239
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               29                177
  MALE                 27                239
[1] 2 2
[1] FALSE
D21V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11Q GAIN MUTATED            17               13                26
  11Q GAIN WILD-TYPE         159              105               152
D21V5, multiclass
                   clus
vv                  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASTROCYTOMA                     17                159
  OLIGOASTROCYTOMA                13                105
  OLIGODENDROGLIOMA               26                152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    11  45
  11Q GAIN WILD-TYPE  81 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     11   45
  11Q GAIN WILD-TYPE   81  335
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                11                 81
  YES               45                335
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           2    51
  11Q GAIN WILD-TYPE                        13   386
D21V7, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          51                386
[1] 4 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, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     2  48
  11Q GAIN WILD-TYPE  16 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2   48
  11Q GAIN WILD-TYPE   16  371
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               48                371
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    22   8
  12P GAIN WILD-TYPE 354  86
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                30                440 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                 86 
$`12P GAIN MUTATED`
TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-A4XE TCGA-DB-A64P TCGA-DH-A669 TCGA-DU-6395 
       81.96        47.93        37.45        30.12        30.21        49.02 
TCGA-DU-6400 TCGA-DU-7007 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY 
        1.22        62.96        19.13         4.96         3.65        12.20 
TCGA-DU-A7T8 TCGA-E1-5304 TCGA-E1-A7YW TCGA-FG-7634 TCGA-FG-8182 TCGA-FG-8191 
      124.50        41.13        36.82        15.35        13.68        32.61 
TCGA-HT-7469 TCGA-HT-7473 TCGA-HT-7604 TCGA-HT-7873 TCGA-HT-7884 TCGA-HT-8018 
       11.54        16.54       122.47        23.61        11.28        37.87 
TCGA-HT-A614 TCGA-QH-A6CV TCGA-S9-A7IZ TCGA-TM-A84I TCGA-WY-A858 TCGA-WY-A85E 
        2.70        14.53         7.13        28.08        43.96        20.81 

$`12P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 
        7.40         6.61       122.73        75.25        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       30.21        46.72        39.78        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       24.20        25.48         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       30.74        16.18        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
        8.02        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       13.12        13.38         3.45        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.73        11.47       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S2 
       14.17        14.24        12.59        15.12         5.65         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
        7.13        21.30        17.98        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.50        44.42         0.56        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       32.45        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       23.97        18.44        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       12.95        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
       27.52         0.10         6.67        40.11         0.13         0.03 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       29.85        23.18         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47         3.72        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55         0.10        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       22.32        23.51        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        40.64        30.44        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        51.06        13.32        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D 
       46.88        37.71 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.22               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            124.50             211.17 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            25.845             18.560 
[1] "1.2 - 124.5 (25.8)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1.2"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    10  20
  12P GAIN WILD-TYPE 196 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     10   20
  12P GAIN WILD-TYPE  196  246
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               10                196
  MALE                 20                246
[1] 2 2
[1] FALSE
D22V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12P GAIN MUTATED            10               11                 9
  12P GAIN WILD-TYPE         166              107               169
D22V5, multiclass
                   clus
vv                  12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASTROCYTOMA                     10                166
  OLIGOASTROCYTOMA                11                107
  OLIGODENDROGLIOMA                9                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     6  24
  12P GAIN WILD-TYPE  86 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6   24
  12P GAIN WILD-TYPE   86  356
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 6                 86
  YES               24                356
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     1
  12P GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           1    28
  12P GAIN WILD-TYPE                        14   409
D22V7, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          28                409
[1] 4 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, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1  27
  12P GAIN WILD-TYPE  17 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   27
  12P GAIN WILD-TYPE   17  392
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               27                392
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED     8   6
  12Q GAIN WILD-TYPE 368  88
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                14                456 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 88 
$`12Q GAIN MUTATED`
TCGA-DH-A669 TCGA-DU-6395 TCGA-DU-6400 TCGA-DU-7007 TCGA-DU-8165 TCGA-DU-A5TT 
       30.21        49.02         1.22        62.96        19.13         4.96 
TCGA-DU-A5TY TCGA-DU-A7TA TCGA-E1-5304 TCGA-FG-7634 TCGA-HT-7873 TCGA-HT-7884 
       12.20        77.88        41.13        15.35        23.61        11.28 
TCGA-QH-A6CV TCGA-S9-A6UA 
       14.53         5.85 

$`12Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       15.16       211.17        52.11        22.42        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       12.59        15.12         3.65         5.65         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       21.30        17.98       124.50        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       44.42         0.56        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       23.97        18.44        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
        0.49        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
       35.47         3.72        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.83        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61        16.08        98.24        95.93       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.22               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             77.88             211.17 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             17.24              18.66 
[1] "1.2 - 77.9 (17.2)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "2.5"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4  10
  12Q GAIN WILD-TYPE 202 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4   10
  12Q GAIN WILD-TYPE  202  256
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                4                202
  MALE                 10                256
[1] 2 2
[1] FALSE
D23V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12Q GAIN MUTATED             5                3                 6
  12Q GAIN WILD-TYPE         171              115               172
D23V5, multiclass
                   clus
vv                  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASTROCYTOMA                      5                171
  OLIGOASTROCYTOMA                 3                115
  OLIGODENDROGLIOMA                6                172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  12
  12Q GAIN WILD-TYPE  90 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   12
  12Q GAIN WILD-TYPE   90  368
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 2                 90
  YES               12                368
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     1
  12Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           0    13
  12Q GAIN WILD-TYPE                        15   424
D23V7, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          13                424
[1] 4 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, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  14
  12Q GAIN WILD-TYPE  18 405
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   14
  12Q GAIN WILD-TYPE   18  405
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               14                405
[1] 2 2
[1] FALSE

Clustering(24) Variable = 13Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     5   0
  13Q GAIN WILD-TYPE 371  94
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                465 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                 94 
$`13Q GAIN MUTATED`
TCGA-HT-7611 TCGA-HT-A5R7 TCGA-QH-A65S TCGA-QH-A6X9 TCGA-VM-A8CA 
       57.60        20.22         2.53         1.91        13.51 

$`13Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 
       17.29         3.16        22.06        45.99        56.09         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34        16.73        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
       15.98        26.99        43.04        30.08         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              1.91               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             57.60             211.17 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             13.51              18.71 
[1] "1.9 - 57.6 (13.5)"  "0.0 - 211.2 (18.7)"
[1] "hr="     "3300000"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     3   3
  13Q GAIN WILD-TYPE 203 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    3
  13Q GAIN WILD-TYPE  203  263
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                3                203
  MALE                  3                263
[1] 2 2
[1] FALSE
D24V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  13Q GAIN MUTATED             2                2                 2
  13Q GAIN WILD-TYPE         174              116               176
D24V5, multiclass
                   clus
vv                  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASTROCYTOMA                      2                174
  OLIGOASTROCYTOMA                 2                116
  OLIGODENDROGLIOMA                2                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   6
  13Q GAIN WILD-TYPE  92 374
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    6
  13Q GAIN WILD-TYPE   92  374
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 0                 92
  YES                6                374
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           0     5
  13Q GAIN WILD-TYPE                        15   432
D24V7, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                           5                432
[1] 4 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, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   5
  13Q GAIN WILD-TYPE  18 414
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    5
  13Q GAIN WILD-TYPE   18  414
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO                5                414
[1] 2 2
[1] FALSE

Clustering(25) Variable = 14Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     2   1
  14Q GAIN WILD-TYPE 374  93
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                467 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 93 
$`14Q GAIN MUTATED`
TCGA-CS-6665 TCGA-DH-A669 TCGA-DU-7019 
       12.43        30.21        26.30 

$`14Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7290 
        6.54         8.84       117.40        90.77        30.67        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.14        16.83        21.40        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             12.43               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             30.21             211.17 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             26.30              18.61 
[1] "12.4 - 30.2 (26.3)" "0.0 - 211.2 (18.6)"
[1] "hr=" "2.3"
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1   2
  14Q GAIN WILD-TYPE 205 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    2
  14Q GAIN WILD-TYPE  205  264
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                1                205
  MALE                  2                264
[1] 2 2
[1] FALSE
D25V4, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                267 
        TCGA-CS-4938         TCGA-CS-4941         TCGA-CS-4942 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-4943         TCGA-CS-4944         TCGA-CS-5390 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-5393         TCGA-CS-5395         TCGA-CS-5396 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-5397         TCGA-CS-6186         TCGA-CS-6188 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-6290         TCGA-CS-6666         TCGA-CS-6667 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-6668         TCGA-CS-6669         TCGA-DB-5274 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A4XE         TCGA-DB-A64L         TCGA-DB-A64Q 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A64R         TCGA-DB-A64S         TCGA-DB-A64U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A64V         TCGA-DB-A64W         TCGA-DB-A64X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A75L         TCGA-DB-A75O         TCGA-DH-5140 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-A66B         TCGA-DH-A66D         TCGA-DH-A66F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-A66G         TCGA-DH-A7UR         TCGA-DH-A7UU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-A7UV         TCGA-DU-5851         TCGA-DU-5852 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5853         TCGA-DU-5854         TCGA-DU-5855 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5870         TCGA-DU-5871         TCGA-DU-5874 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6396         TCGA-DU-6403         TCGA-DU-6404 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6405         TCGA-DU-6407         TCGA-DU-6408 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6410         TCGA-DU-7011         TCGA-DU-7013 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7014         TCGA-DU-7015         TCGA-DU-7018 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7294         TCGA-DU-7298         TCGA-DU-7299 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7300         TCGA-DU-7301         TCGA-DU-7302 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7304         TCGA-DU-7306         TCGA-DU-7309 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8158         TCGA-DU-8161         TCGA-DU-8162 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8163         TCGA-DU-8165         TCGA-DU-8167 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8168         TCGA-DU-A5TP         TCGA-DU-A5TR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A5TS         TCGA-DU-A5TU         TCGA-DU-A5TW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A6S2         TCGA-DU-A6S6         TCGA-DU-A6S7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A6S8         TCGA-DU-A76R         TCGA-DU-A7T6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A7T8         TCGA-DU-A7TA         TCGA-DU-A7TB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A7TC         TCGA-DU-A7TD         TCGA-DU-A7TG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5305         TCGA-E1-5307         TCGA-E1-5311 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5319         TCGA-E1-5322 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-A7YO         TCGA-E1-A7YV         TCGA-E1-A7YW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-A7Z6         TCGA-FG-5963         TCGA-FG-5965 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-6688         TCGA-FG-6689         TCGA-FG-6690 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-6691         TCGA-FG-7636         TCGA-FG-7638 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-8181         TCGA-FG-8185         TCGA-FG-8186 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-8187         TCGA-FG-8188         TCGA-FG-8189 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A4MT         TCGA-FG-A4MW         TCGA-FG-A4MX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A60J         TCGA-FG-A60L         TCGA-FG-A6J1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A6J3         TCGA-FG-A711         TCGA-FG-A713 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A87Q         TCGA-HT-7468         TCGA-HT-7470 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7475         TCGA-HT-7477         TCGA-HT-7485 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7607         TCGA-HT-7609         TCGA-HT-7611 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7689         TCGA-HT-7692         TCGA-HT-7693 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7694         TCGA-HT-7854         TCGA-HT-7875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7884         TCGA-HT-8564         TCGA-HT-A4DV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-A5R7         TCGA-HT-A5RA         TCGA-HT-A5RC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-A615         TCGA-HT-A617         TCGA-HT-A618 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-A61B         TCGA-HT-A61C         TCGA-HT-A74L 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IK-7675         TCGA-KT-A74X         TCGA-KT-A7W1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5EU         TCGA-P5-A5EV         TCGA-P5-A5EW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5EX         TCGA-P5-A5F0         TCGA-P5-A5F2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5F4         TCGA-P5-A5F6         TCGA-P5-A731 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A65R         TCGA-QH-A65S         TCGA-QH-A65V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A65X         TCGA-QH-A65Z         TCGA-QH-A6CS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6CU         TCGA-QH-A6CV         TCGA-QH-A6CW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6CX         TCGA-QH-A6CY         TCGA-QH-A6CZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6X3         TCGA-QH-A6X4         TCGA-QH-A6X5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6X8         TCGA-QH-A6X9         TCGA-QH-A6XA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6XC         TCGA-QH-A86X         TCGA-QH-A870 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-RY-A83Y         TCGA-RY-A840         TCGA-RY-A845 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-RY-A847         TCGA-S9-A6TS         TCGA-S9-A6TU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6TV         TCGA-S9-A6TW         TCGA-S9-A6TX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6TY         TCGA-S9-A6TZ         TCGA-S9-A6U0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6U1         TCGA-S9-A6U2         TCGA-S9-A6U5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6U6         TCGA-S9-A6U8         TCGA-S9-A6UA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6UB         TCGA-S9-A6WD         TCGA-S9-A6WE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6WG         TCGA-S9-A6WH         TCGA-S9-A6WI 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6WL         TCGA-S9-A6WM         TCGA-S9-A6WN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6WO         TCGA-S9-A6WP         TCGA-S9-A6WQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7IQ         TCGA-S9-A7IS         TCGA-S9-A7IX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7IY         TCGA-S9-A7IZ         TCGA-S9-A7J0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7J1         TCGA-S9-A7J2         TCGA-S9-A7J3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7QW         TCGA-S9-A7QX         TCGA-S9-A7QY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7QZ         TCGA-S9-A7R1         TCGA-S9-A7R2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7R3         TCGA-S9-A7R4         TCGA-S9-A7R7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7R8         TCGA-S9-A89V         TCGA-S9-A89Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A7C3         TCGA-TM-A7C4         TCGA-TM-A7C5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A7CA         TCGA-TM-A7CF         TCGA-TM-A84B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A84C         TCGA-TM-A84F         TCGA-TM-A84G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A84H         TCGA-TM-A84I         TCGA-TM-A84J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A84L         TCGA-TM-A84M         TCGA-TM-A84O 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A84Q         TCGA-TM-A84R         TCGA-TM-A84S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A84T         TCGA-TQ-A7RW         TCGA-VM-A8C8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-VM-A8CA         TCGA-VM-A8CD         TCGA-VM-A8CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-VM-A8CH         TCGA-WY-A858         TCGA-WY-A859 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  14Q GAIN MUTATED             1                1                 1
  14Q GAIN WILD-TYPE         175              117               177
D25V5, multiclass
                   clus
vv                  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASTROCYTOMA                      1                175
  OLIGOASTROCYTOMA                 1                117
  OLIGODENDROGLIOMA                1                177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   1
  14Q GAIN WILD-TYPE  90 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    1
  14Q GAIN WILD-TYPE   90  379
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 2                 90
  YES                1                379
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     0
  14Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           0     3
  14Q GAIN WILD-TYPE                        15   434
D25V7, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                           3                434
[1] 4 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, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0   3
  14Q GAIN WILD-TYPE  18 416
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    3
  14Q GAIN WILD-TYPE   18  416
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO                3                416
[1] 2 2
[1] FALSE

Clustering(26) Variable = 15Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     4   5
  15Q GAIN WILD-TYPE 372  89
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                461 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 89 
$`15Q GAIN MUTATED`
TCGA-CS-4943 TCGA-DU-5852 TCGA-DU-7014 TCGA-DU-7306 TCGA-E1-5304 TCGA-E1-A7YV 
       18.15         6.74       117.40        41.98        41.13        32.45 
TCGA-HT-7477 TCGA-S9-A6UA TCGA-S9-A7IZ 
       24.26         5.85         7.13 

$`15Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
        3.45        18.61        18.02        14.56        17.46        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
       95.57       130.78        75.02        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.03        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61        16.08        98.24        95.93       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       22.32        23.51        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              5.85               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            117.40             211.17 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             24.26              18.61 
[1] "5.8 - 117.4 (24.3)" "0.0 - 211.2 (18.6)"
[1] "hr=" "2.4"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3   6
  15Q GAIN WILD-TYPE 203 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    6
  15Q GAIN WILD-TYPE  203  260
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                203
  MALE                  6                260
[1] 2 2
[1] FALSE
D26V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  15Q GAIN MUTATED             5                3                 1
  15Q GAIN WILD-TYPE         171              115               177
D26V5, multiclass
                   clus
vv                  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASTROCYTOMA                      5                171
  OLIGOASTROCYTOMA                 3                115
  OLIGODENDROGLIOMA                1                177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2   7
  15Q GAIN WILD-TYPE  90 373
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    7
  15Q GAIN WILD-TYPE   90  373
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 2                 90
  YES                7                373
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     0
  15Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           0     9
  15Q GAIN WILD-TYPE                        15   428
D26V7, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                           9                428
[1] 4 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, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0   8
  15Q GAIN WILD-TYPE  18 411
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    8
  15Q GAIN WILD-TYPE   18  411
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO                8                411
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    11   5
  16P GAIN WILD-TYPE 365  89
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                454 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 89 
$`16P GAIN MUTATED`
TCGA-CS-5397 TCGA-DB-A4XH TCGA-DH-A66B TCGA-DU-6392 TCGA-DU-6400 TCGA-DU-7007 
        6.38        31.63        42.05       211.17         1.22        62.96 
TCGA-DU-7010 TCGA-DU-A5TS TCGA-E1-5304 TCGA-FG-5962 TCGA-HT-A5R7 TCGA-HT-A618 
       14.99        15.12        41.13        47.77        20.22        16.83 
TCGA-S9-A6WH TCGA-S9-A7QW TCGA-TM-A84I TCGA-VM-A8CA 
       32.45        15.06        28.08        13.51 

$`16P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         9.96        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        30.21        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 
      114.08         7.96         7.73        11.47       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT 
       16.96        15.48        14.17        14.24        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       44.42         0.56        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
       36.82        32.35        14.33         0.23         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        26.04         0.13         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 
        5.33         2.70        16.93         1.81        16.14        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL 
      106.39        69.50        72.59        80.12        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        17.03        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       24.92        16.18        59.05        40.64        30.44        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB 
       23.80        15.98        26.99        43.04        30.08         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              1.22               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            211.17             182.33 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             24.15              18.61 
[1] "1.2 - 211.2 (24.1)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.2"
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     9   7
  16P GAIN WILD-TYPE 197 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    7
  16P GAIN WILD-TYPE  197  259
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                9                197
  MALE                  7                259
[1] 2 2
[1] FALSE
D27V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16P GAIN MUTATED            10                2                 4
  16P GAIN WILD-TYPE         166              116               174
D27V5, multiclass
                   clus
vv                  16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASTROCYTOMA                     10                166
  OLIGOASTROCYTOMA                 2                116
  OLIGODENDROGLIOMA                4                174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     4  12
  16P GAIN WILD-TYPE  88 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4   12
  16P GAIN WILD-TYPE   88  368
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                 88
  YES               12                368
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     0
  16P GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           1    14
  16P GAIN WILD-TYPE                        14   423
D27V7, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          14                423
[1] 4 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, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  15
  16P GAIN WILD-TYPE  18 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   15
  16P GAIN WILD-TYPE   18  404
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               15                404
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    12   6
  16Q GAIN WILD-TYPE 364  88
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                452 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 88 
$`16Q GAIN MUTATED`
TCGA-CS-5397 TCGA-DB-A4XH TCGA-DU-6392 TCGA-DU-6400 TCGA-DU-7007 TCGA-DU-7010 
        6.38        31.63       211.17         1.22        62.96        14.99 
TCGA-DU-A5TS TCGA-E1-5302 TCGA-E1-5304 TCGA-FG-5962 TCGA-HT-A5R7 TCGA-HT-A616 
       15.12        50.14        41.13        47.77        20.22         1.81 
TCGA-HT-A618 TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-TM-A84I TCGA-TM-A84Q TCGA-VM-A8CA 
       16.83        20.02        15.06        28.08        25.38        13.51 

$`16Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         9.96        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
      138.28       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
        7.50        44.42         0.56        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
       36.82        32.35        14.33         0.23         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        26.04         0.13         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61B 
        5.33         2.70        16.93        16.14        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        22.32        23.51         7.13         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       17.03        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        40.64        30.44        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       24.79        33.24        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       26.99        43.04        30.08         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              1.22               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            211.17             182.33 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             20.12              18.61 
[1] "1.2 - 211.2 (20.1)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.4"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    10   8
  16Q GAIN WILD-TYPE 196 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    8
  16Q GAIN WILD-TYPE  196  258
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               10                196
  MALE                  8                258
[1] 2 2
[1] FALSE
D28V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16Q GAIN MUTATED            12                1                 5
  16Q GAIN WILD-TYPE         164              117               173
D28V5, multiclass
                   clus
vv                  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASTROCYTOMA                     12                164
  OLIGOASTROCYTOMA                 1                117
  OLIGODENDROGLIOMA                5                173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     5  13
  16Q GAIN WILD-TYPE  87 367
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5   13
  16Q GAIN WILD-TYPE   87  367
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 5                 87
  YES               13                367
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           1    16
  16Q GAIN WILD-TYPE                        14   421
D28V7, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          16                421
[1] 4 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, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  17
  16Q GAIN WILD-TYPE  18 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   17
  16Q GAIN WILD-TYPE   18  402
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               17                402
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    12   6
  17P GAIN WILD-TYPE 364  88
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                18                452 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 6                 88 
$`17P GAIN MUTATED`
TCGA-CS-6665 TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-7013 TCGA-DU-A6S7 TCGA-E1-5304 
       12.43        30.21        17.19         8.84         7.23        41.13 
TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A6J3 TCGA-HT-7477 TCGA-IK-7675 TCGA-QH-A6CV 
       47.77        15.35        22.26        24.26        19.00        14.53 
TCGA-S9-A6TS TCGA-S9-A6U1 TCGA-S9-A6WL TCGA-TM-A84M TCGA-VM-A8CA TCGA-VW-A8FI 
       62.17        17.62        31.10        24.79        13.51         8.05 

$`17P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        42.05        27.81 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       12.20         8.65         2.70        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 
       14.93        24.99        23.97        18.44        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        19.33        14.83        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
        2.07        19.59        30.67        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 
       34.49        31.33        28.70        22.95        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
       15.98        26.99        43.04        30.08         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       35.93        23.47        37.05        16.01        23.21        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              7.23               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             62.17             211.17 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             18.31              18.66 
[1] "7.2 - 62.2 (18.3)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "2.4"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     5  13
  17P GAIN WILD-TYPE 201 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5   13
  17P GAIN WILD-TYPE  201  253
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                5                201
  MALE                 13                253
[1] 2 2
[1] FALSE
D29V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17P GAIN MUTATED            10                1                 7
  17P GAIN WILD-TYPE         166              117               171
D29V5, multiclass
                   clus
vv                  17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASTROCYTOMA                     10                166
  OLIGOASTROCYTOMA                 1                117
  OLIGODENDROGLIOMA                7                171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4  14
  17P GAIN WILD-TYPE  88 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4   14
  17P GAIN WILD-TYPE   88  366
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 4                 88
  YES               14                366
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     1
  17P GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           0    16
  17P GAIN WILD-TYPE                        15   421
D29V7, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          16                421
[1] 4 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, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  16
  17P GAIN WILD-TYPE  17 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   16
  17P GAIN WILD-TYPE   17  403
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               16                403
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    13   7
  17Q GAIN WILD-TYPE 363  87
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                20                450 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 87 
$`17Q GAIN MUTATED`
TCGA-CS-6665 TCGA-DB-A64Q TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-7013 TCGA-DU-A6S7 
       12.43         5.98        30.21        17.19         8.84         7.23 
TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-7634 TCGA-HT-7477 TCGA-IK-7675 TCGA-QH-A6CV 
       41.13        47.77        15.35        24.26        19.00        14.53 
TCGA-S9-A6TS TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A6WL TCGA-TM-A84M TCGA-VM-A8CA 
       62.17        17.62         5.85        31.10        24.79        13.51 
TCGA-VM-A8CH TCGA-VW-A8FI 
       23.47         8.05 

$`17Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64R 
       72.95        31.63        24.20        25.48        30.12        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G 
       30.31        14.40         8.02        42.05        27.81        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        13.12        13.38         3.45        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 
      156.23       138.28        14.99       105.21         6.54       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70        77.98         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       24.99        23.97        18.44        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        19.33        14.83        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
        2.07        19.59        30.67        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 
       34.49        31.33        28.70        22.95        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       16.08        98.24        95.93       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       80.12        32.45        84.99        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       26.99        43.04        30.08         0.10         7.89        35.93 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       37.05        16.01        23.21        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              5.85               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             62.17             211.17 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            17.405             18.710 
[1] "5.8 - 62.2 (17.4)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "2.8"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6  14
  17Q GAIN WILD-TYPE 200 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6   14
  17Q GAIN WILD-TYPE  200  252
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                6                200
  MALE                 14                252
[1] 2 2
[1] FALSE
D30V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17Q GAIN MUTATED            11                2                 7
  17Q GAIN WILD-TYPE         165              116               171
D30V5, multiclass
                   clus
vv                  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASTROCYTOMA                     11                165
  OLIGOASTROCYTOMA                 2                116
  OLIGODENDROGLIOMA                7                171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4  16
  17Q GAIN WILD-TYPE  88 364
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   16
  17Q GAIN WILD-TYPE   88  364
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 4                 88
  YES               16                364
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     1
  17Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           0    17
  17Q GAIN WILD-TYPE                        15   420
D30V7, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          17                420
[1] 4 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, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  16
  17Q GAIN WILD-TYPE  17 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   16
  17Q GAIN WILD-TYPE   17  403
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               16                403
[1] 2 2
[1] FALSE

Clustering(31) Variable = 18P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    11   4
  18P GAIN WILD-TYPE 365  90
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                455 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 90 
$`18P GAIN MUTATED`
TCGA-CS-4938 TCGA-DB-5277 TCGA-DH-A7UT TCGA-DU-7010 TCGA-DU-8165 TCGA-DU-A5TS 
        4.70        50.86        13.38        14.99        19.13        15.12 
TCGA-DU-A5TY TCGA-E1-5304 TCGA-E1-A7YV TCGA-HT-8111 TCGA-HW-7489 TCGA-QH-A6CS 
       12.20        41.13        32.45         0.23         8.32        19.33 
TCGA-QH-A6X9 TCGA-S9-A89Z TCGA-WY-A85E 
        1.91        11.97        20.81 

$`18P GAIN WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        7.69        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        54.25        13.12         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       12.59         4.96         3.65         5.65         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.50        44.42         0.56        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        5.56        13.78        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 
       15.35        11.05         0.10        29.92        19.89        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA 
        9.17        10.29        14.53        16.34        16.73        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       18.71        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       39.88        43.40        45.80        46.88        37.71 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.23               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             50.86             211.17 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             14.99              18.71 
[1] "0.2 - 50.9 (15.0)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "2.5"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     7   8
  18P GAIN WILD-TYPE 199 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7    8
  18P GAIN WILD-TYPE  199  258
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                7                199
  MALE                  8                258
[1] 2 2
[1] FALSE
D31V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18P GAIN MUTATED             8                4                 3
  18P GAIN WILD-TYPE         168              114               175
D31V5, multiclass
                   clus
vv                  18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASTROCYTOMA                      8                168
  OLIGOASTROCYTOMA                 4                114
  OLIGODENDROGLIOMA                3                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  13
  18P GAIN WILD-TYPE  90 367
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   13
  18P GAIN WILD-TYPE   90  367
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 2                 90
  YES               13                367
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           1    14
  18P GAIN WILD-TYPE                        14   423
D31V7, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          14                423
[1] 4 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, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  14
  18P GAIN WILD-TYPE  18 405
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   14
  18P GAIN WILD-TYPE   18  405
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               14                405
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     7   3
  18Q GAIN WILD-TYPE 369  91
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                460 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 91 
$`18Q GAIN MUTATED`
TCGA-DU-7010 TCGA-DU-8165 TCGA-DU-A5TS TCGA-DU-A5TY TCGA-E1-5304 TCGA-E1-A7YV 
       14.99        19.13        15.12        12.20        41.13        32.45 
TCGA-HT-8111 TCGA-HW-7489 TCGA-QH-A6CS TCGA-S9-A89Z 
        0.23         8.32        19.33        11.97 

$`18Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        5.10        23.74        14.60        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
        5.65         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
       95.57       130.78        75.02        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 
        0.10         0.46         2.50         5.56        13.78        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       29.92        19.89        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        15.85        14.04        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 
       99.06        30.05        98.63        31.59        18.71        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.23               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             41.13             211.17 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            15.055             18.710 
[1] "0.2 - 41.1 (15.1)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "2.9"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4   6
  18Q GAIN WILD-TYPE 202 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    6
  18Q GAIN WILD-TYPE  202  260
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                202
  MALE                  6                260
[1] 2 2
[1] FALSE
D32V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18Q GAIN MUTATED             5                3                 2
  18Q GAIN WILD-TYPE         171              115               176
D32V5, multiclass
                   clus
vv                  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASTROCYTOMA                      5                171
  OLIGOASTROCYTOMA                 3                115
  OLIGODENDROGLIOMA                2                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1   9
  18Q GAIN WILD-TYPE  91 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    9
  18Q GAIN WILD-TYPE   91  371
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 1                 91
  YES                9                371
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           1     9
  18Q GAIN WILD-TYPE                        14   428
D32V7, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                           9                428
[1] 4 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, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  10
  18Q GAIN WILD-TYPE  18 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   10
  18Q GAIN WILD-TYPE   18  409
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               10                409
[1] 2 2
[1] FALSE

Clustering(33) Variable = 19P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    71  19
  19P GAIN WILD-TYPE 305  75
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                90                380 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                19                 75 
$`19P GAIN MUTATED`
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6668 TCGA-DB-5274 
       21.01         9.96        17.69        23.84         8.02        75.25 
TCGA-DB-5278 TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64R 
       50.17        39.78        72.95        24.20        30.12        31.40 
TCGA-DB-A75L TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-5854 TCGA-DU-5874 TCGA-DU-6393 
       11.24        30.21        17.19         8.45        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6406 TCGA-DU-7009 TCGA-DU-7015 
       22.42        46.06         1.22        16.83       138.28        90.77 
TCGA-DU-7019 TCGA-DU-7298 TCGA-DU-7306 TCGA-DU-8164 TCGA-DU-A5TT TCGA-DU-A6S2 
       26.30        18.94        41.98        21.40         4.96         8.65 
TCGA-DU-A76K TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-A7YO TCGA-FG-5962 TCGA-FG-6692 
       11.41         0.56        41.13        75.02        47.77        18.44 
TCGA-FG-7643 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60K 
       20.09        16.01        14.96        10.72        18.38        17.82 
TCGA-FG-A87Q TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7480 TCGA-HT-7687 TCGA-HT-7695 
        5.72         6.67        11.54        75.19         0.10        14.53 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7875 TCGA-HT-7882 TCGA-HT-8012 TCGA-HT-8104 
        0.49        23.61         0.33         3.72         9.40        12.23 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A61B TCGA-HW-7495 TCGA-KT-A7W1 
       27.35         5.33        16.93        17.52         4.31        14.40 
TCGA-P5-A5F0 TCGA-P5-A72U TCGA-P5-A730 TCGA-QH-A65X TCGA-QH-A6CV TCGA-QH-A6CZ 
        4.11         0.16         0.20        15.85        14.53         9.17 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A73M TCGA-RY-A83X 
        5.03        11.08        88.83        94.03        59.38        30.87 
TCGA-RY-A83Y TCGA-S9-A6TV TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6WE TCGA-S9-A6WM 
        5.46        18.77        31.33        23.64        72.59        19.86 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C3 TCGA-TM-A84B 
        8.19         2.04        13.02       169.84        49.45        24.92 
TCGA-TM-A84G TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VW-A7QS TCGA-W9-A837 
       40.64        13.51         0.10        35.93        23.21        51.06 

$`19P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5397 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
       40.18         0.10         6.38        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        7.56         7.40         6.61       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.86        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XH 
       18.84        30.21        46.72        37.45        33.57        31.63 
TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
       25.48         5.98        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       18.51        12.10        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        42.05        27.81 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 
       18.02        14.56        17.46         6.74        13.38         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 
      182.33        18.94        17.49       211.17        49.02        75.16 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      156.23        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 
       30.67        10.36         7.96        94.32        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        60.30        23.31         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       14.60        20.68        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59        15.12         3.65         5.65        12.20 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76O 
        2.70        77.98         7.23         5.98        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
        7.50        44.42        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YV TCGA-E1-A7YW 
      134.27        78.21        95.57       130.78        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       32.35        14.33         0.23         0.20        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
       36.82        18.77        14.93        24.99        23.97        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       17.88        22.55        20.61        12.95        13.68        14.24 
TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       20.09        22.52        32.61        38.27        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       14.76        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 
       10.78        36.66        48.69        20.45        13.58        27.52 
TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        0.10        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 
       17.42         6.54        24.26         6.38        40.34        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 
        0.76        44.68         6.05        42.74        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7854 
        0.10         0.10         2.96        17.52         6.90        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7877 
       19.23        39.09         0.23        50.63        37.15         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33        35.47        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
       16.24        63.55         0.10        37.87        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 
        0.13        20.22         0.07         0.10         2.70         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.14        16.83        21.40        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18        35.90        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       42.77        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W 
        2.30         5.88         7.63         0.76         1.28        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       13.25        11.64         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX 
       12.62        14.04        19.33        14.83        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        2.20        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A870 TCGA-R8-A6MO TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       16.50        12.99        32.65         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX 
       19.59        30.67        62.17        87.12        37.84        34.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       28.70        22.95        17.62        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WG TCGA-S9-A6WH 
       95.93         5.85       106.39        69.50        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-S9-A7R3 
       17.03        15.06        13.12        28.37        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 
       30.05        98.63        31.59        18.71        11.97        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H 
       49.32        34.78        48.39        16.18        59.05        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A8FI 
       30.08         7.89        23.47        37.05        16.01         8.05 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.10               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            169.84             211.17 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            17.755             18.805 
[1] "0.1 - 169.8 (17.8)" "0.0 - 211.2 (18.8)"
[1] "hr=" "1.1"
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    36  55
  19P GAIN WILD-TYPE 170 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     36   55
  19P GAIN WILD-TYPE  170  211
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               36                170
  MALE                 55                211
[1] 2 2
[1] FALSE
D33V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19P GAIN MUTATED            18               17                56
  19P GAIN WILD-TYPE         158              101               122
D33V5, multiclass
                   clus
vv                  19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASTROCYTOMA                     18                158
  OLIGOASTROCYTOMA                17                101
  OLIGODENDROGLIOMA               56                122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    16  75
  19P GAIN WILD-TYPE  76 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16   75
  19P GAIN WILD-TYPE   76  305
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                16                 76
  YES               75                305
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     2
  19P GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           4    82
  19P GAIN WILD-TYPE                        11   355
D33V7, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  6
  BLACK OR AFRICAN AMERICAN                       4                 11
  WHITE                                          82                355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     4  82
  19P GAIN WILD-TYPE  14 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4   82
  19P GAIN WILD-TYPE   14  337
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 14
  NOT HISPANIC OR LATINO               82                337
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    14   8
  19Q GAIN WILD-TYPE 362  86
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                448 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 8                 86 
$`19Q GAIN MUTATED`
TCGA-CS-5395 TCGA-CS-6186 TCGA-DU-6402 TCGA-DU-6406 TCGA-DU-7019 TCGA-DU-A76K 
       21.01        17.69         7.04        16.83        26.30        11.41 
TCGA-DU-A7TJ TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-HT-7860 
        0.56        18.44        20.09        10.72        18.38         0.49 
TCGA-HT-7873 TCGA-HT-7882 TCGA-HT-8104 TCGA-HT-A5RA TCGA-KT-A7W1 TCGA-P5-A72U 
       23.61         3.72        12.23        27.35        14.40         0.16 
TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6WM TCGA-TM-A7C3 
       14.53         5.03        19.86        49.45 

$`19Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6290 
       40.18         0.10         9.96         6.38        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       12.43         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75         1.22        87.45        11.64       133.74        19.89 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
      117.40        90.77        30.67        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L 
        8.65         2.70        77.98         7.23         5.98        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       23.51         7.50        44.42        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       14.93        24.99        23.97        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.61        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       14.96        22.52        32.61        38.27        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7874 
       39.48        19.23        39.09         0.23        50.63        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
        0.33         0.13         3.68         5.33        35.47        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        42.77        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        1.28        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.83        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        31.10        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.16               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             49.45             211.17 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            15.680             18.805 
[1] "0.2 - 49.5 (15.7)"  "0.0 - 211.2 (18.8)"
[1] "hr=" "4.5"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     9  13
  19Q GAIN WILD-TYPE 197 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9   13
  19Q GAIN WILD-TYPE  197  253
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                9                197
  MALE                 13                253
[1] 2 2
[1] FALSE
D34V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19Q GAIN MUTATED             9                8                 5
  19Q GAIN WILD-TYPE         167              110               173
D34V5, multiclass
                   clus
vv                  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASTROCYTOMA                      9                167
  OLIGOASTROCYTOMA                 8                110
  OLIGODENDROGLIOMA                5                173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     5  17
  19Q GAIN WILD-TYPE  87 363
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5   17
  19Q GAIN WILD-TYPE   87  363
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 5                 87
  YES               17                363
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     1
  19Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           2    19
  19Q GAIN WILD-TYPE                        13   418
D34V7, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          19                418
[1] 4 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, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  20
  19Q GAIN WILD-TYPE  17 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   20
  19Q GAIN WILD-TYPE   17  399
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               20                399
[1] 2 2
[1] FALSE

Clustering(35) Variable = 20P GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    24  14
  20P GAIN WILD-TYPE 352  80
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                38                432 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                14                 80 
$`20P GAIN MUTATED`
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-A75O TCGA-DH-A669 
       21.01         6.38        23.84        12.43        30.74        30.21 
TCGA-DH-A66B TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5871 TCGA-DU-6400 TCGA-DU-6406 
       42.05         6.74         8.45        18.94         1.22        16.83 
TCGA-DU-7298 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A6S7 
       18.94        14.60        19.13         4.96        12.20         7.23 
TCGA-DU-A76K TCGA-DU-A76L TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A4MU 
       11.41        26.76        41.13        47.77        15.35        10.72 
TCGA-HT-7474 TCGA-HT-7477 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8104 TCGA-HT-A5RC 
        3.75        24.26         0.49         3.72        12.23         5.33 
TCGA-HT-A74H TCGA-HW-A5KK TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6WH TCGA-S9-A6WM 
        2.43        12.76        14.53         5.03        32.45        19.86 
TCGA-TM-A7C3 TCGA-VM-A8CA 
       49.45        13.51 

$`20P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6666 
       40.18         0.10         9.96        17.69        17.95         8.48 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
        7.56         8.02         7.40         6.61       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
       75.25        47.93        72.92        50.86        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       39.78        37.45        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       16.18        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
        3.45        18.61        18.02        14.56        17.46        13.38 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 
       30.67        26.30        10.36         7.96        94.32        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
        5.10        23.74        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         3.65         5.65 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R 
        8.65         2.70        77.98         5.98         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       44.42         0.56        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
       36.82        32.35        14.33         0.23         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       18.44        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       32.61        38.27        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
        0.03        16.54        17.42         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        0.23        50.63        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33        35.47        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59        34.19        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.52        17.65        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 
       16.34        16.73         1.91        16.50        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        18.71        11.97        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.49               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             49.45             211.17 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            14.020             18.805 
[1] "0.5 - 49.5 (14.0)"  "0.0 - 211.2 (18.8)"
[1] "hr=" "4.3"
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    18  20
  20P GAIN WILD-TYPE 188 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     18   20
  20P GAIN WILD-TYPE  188  246
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               18                188
  MALE                 20                246
[1] 2 2
[1] FALSE
D35V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20P GAIN MUTATED            19                8                11
  20P GAIN WILD-TYPE         157              110               167
D35V5, multiclass
                   clus
vv                  20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASTROCYTOMA                     19                157
  OLIGOASTROCYTOMA                 8                110
  OLIGODENDROGLIOMA               11                167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     7  31
  20P GAIN WILD-TYPE  85 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7   31
  20P GAIN WILD-TYPE   85  349
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 7                 85
  YES               31                349
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     1
  20P GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           2    34
  20P GAIN WILD-TYPE                        13   403
D35V7, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          34                403
[1] 4 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, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1  34
  20P GAIN WILD-TYPE  17 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   34
  20P GAIN WILD-TYPE   17  385
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               34                385
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    24  14
  20Q GAIN WILD-TYPE 352  80
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                38                432 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                14                 80 
$`20Q GAIN MUTATED`
TCGA-CS-4938 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 
        4.70        21.01         6.38        17.69        23.84        12.43 
TCGA-DH-A669 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5871 TCGA-DU-6400 TCGA-DU-6406 
       30.21         6.74         8.45        18.94         1.22        16.83 
TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76K 
       14.60        19.13         4.96        12.20         7.23        11.41 
TCGA-DU-A76L TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A4MU TCGA-HT-7477 
       26.76        41.13        47.77        15.35        10.72        24.26 
TCGA-HT-7693 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8104 TCGA-HT-8563 TCGA-HT-A5RC 
       17.52         0.49         3.72        12.23        28.27         5.33 
TCGA-HT-A74H TCGA-HW-A5KK TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6WH TCGA-S9-A6WM 
        2.43        12.76        14.53         5.03        32.45        19.86 
TCGA-TM-A7C3 TCGA-VM-A8CA 
       49.45        13.51 

$`20Q GAIN WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        7.69        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
        0.10         9.96        17.95         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
        3.45        18.61        18.02        14.56        17.46        13.38 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        2.76         5.10        23.74        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76O 
        5.65         8.65         2.70        77.98         5.98         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.50        44.42         0.56        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       23.97        18.44        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       22.52        32.61        38.27        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10         2.96         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23        50.63        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 
        0.13         3.68         5.33        35.47        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS 
       13.78         0.23        29.59        34.19        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.52        17.65        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 
       16.34        16.73         1.91        16.50        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        18.71        11.97        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.49               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             49.45             211.17 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             14.02              18.97 
[1] "0.5 - 49.5 (14.0)"  "0.0 - 211.2 (19.0)"
[1] "hr=" "4.7"
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    20  18
  20Q GAIN WILD-TYPE 186 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     20   18
  20Q GAIN WILD-TYPE  186  248
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               20                186
  MALE                 18                248
[1] 2 2
[1] FALSE
D36V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20Q GAIN MUTATED            18                8                12
  20Q GAIN WILD-TYPE         158              110               166
D36V5, multiclass
                   clus
vv                  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASTROCYTOMA                     18                158
  OLIGOASTROCYTOMA                 8                110
  OLIGODENDROGLIOMA               12                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     8  30
  20Q GAIN WILD-TYPE  84 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8   30
  20Q GAIN WILD-TYPE   84  350
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 8                 84
  YES               30                350
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     1
  20Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           1    35
  20Q GAIN WILD-TYPE                        14   402
D36V7, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          35                402
[1] 4 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, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     1  34
  20Q GAIN WILD-TYPE  17 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1   34
  20Q GAIN WILD-TYPE   17  385
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               34                385
[1] 2 2
[1] FALSE

Clustering(37) Variable = 21Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    15   8
  21Q GAIN WILD-TYPE 361  86
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                23                447 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 8                 86 
$`21Q GAIN MUTATED`
TCGA-DB-5277 TCGA-DB-A64W TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-6407 
       50.86        14.40       211.17        52.11         1.22        94.52 
TCGA-DU-8158 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76K TCGA-E1-5304 
        5.10         4.96        12.20         7.23        11.41        41.13 
TCGA-FG-5962 TCGA-FG-7634 TCGA-HT-7605 TCGA-HT-A5RA TCGA-HT-A74H TCGA-HT-A74L 
       47.77        15.35         4.57        27.35         2.43        11.05 
TCGA-QH-A6CV TCGA-QH-A6X9 TCGA-S9-A6WH TCGA-S9-A6WL TCGA-TM-A84H 
       14.53         1.91        32.45        31.10        30.44 

$`21Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        16.83       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        2.76        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 
        3.65         5.65         8.65         2.70        77.98         5.98 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 
       14.93        24.99        23.97        18.44        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       29.85        23.18       122.47        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74J TCGA-HT-A74K 
       16.83        21.40        17.52        17.65        10.52        15.35 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.83        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC 
       10.29        14.53        16.34        16.73        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       72.59        80.12        84.99        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       59.05        40.64        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.22               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            211.17             182.33 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             14.53              18.71 
[1] "1.2 - 211.2 (14.5)" "0.0 - 182.3 (18.7)"
[1] "hr=" "1.6"
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    12  11
  21Q GAIN WILD-TYPE 194 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     12   11
  21Q GAIN WILD-TYPE  194  255
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               12                194
  MALE                 11                255
[1] 2 2
[1] FALSE
D37V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  21Q GAIN MUTATED             9                5                 9
  21Q GAIN WILD-TYPE         167              113               169
D37V5, multiclass
                   clus
vv                  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASTROCYTOMA                      9                167
  OLIGOASTROCYTOMA                 5                113
  OLIGODENDROGLIOMA                9                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     5  18
  21Q GAIN WILD-TYPE  87 362
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5   18
  21Q GAIN WILD-TYPE   87  362
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 5                 87
  YES               18                362
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     1
  21Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           0    22
  21Q GAIN WILD-TYPE                        15   415
D37V7, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          22                415
[1] 4 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, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  23
  21Q GAIN WILD-TYPE  18 396
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   23
  21Q GAIN WILD-TYPE   18  396
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               23                396
[1] 2 2
[1] FALSE

Clustering(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    15   2
  22Q GAIN WILD-TYPE 361  92
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                453 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 92 
$`22Q GAIN MUTATED`
TCGA-CS-6665 TCGA-CS-6668 TCGA-DU-6393 TCGA-DU-6400 TCGA-FG-5962 TCGA-HT-7468 
       12.43         8.02        52.11         1.22        47.77         6.67 
TCGA-HT-8012 TCGA-QH-A6CZ TCGA-R8-A6ML TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A847 
        9.40         9.17        94.03        59.38        30.87        30.67 
TCGA-S9-A6WM TCGA-TM-A84J TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VV-A829 
       19.86        24.16        13.51         0.10        37.05 

$`22Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         8.48         7.56         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
      211.17        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       32.35        14.33         0.23         0.20        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        5.72        27.52         0.10        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8013 
        3.72        11.28        31.43         1.64        16.24        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 
       14.83        14.53        13.61        12.23         2.20        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6MO TCGA-RY-A83Y TCGA-RY-A83Z 
       11.08        12.99        88.83        32.65         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       28.08         2.07        19.59        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       28.08        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
        7.89        35.93        23.47        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.10               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             94.03             211.17 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             19.86              18.61 
[1] "0.1 - 94.0 (19.9)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.6"
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     7  10
  22Q GAIN WILD-TYPE 199 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      7   10
  22Q GAIN WILD-TYPE  199  256
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                7                199
  MALE                 10                256
[1] 2 2
[1] FALSE
D38V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  22Q GAIN MUTATED             2                2                13
  22Q GAIN WILD-TYPE         174              116               165
D38V5, multiclass
                   clus
vv                  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASTROCYTOMA                      2                174
  OLIGOASTROCYTOMA                 2                116
  OLIGODENDROGLIOMA               13                165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  14
  22Q GAIN WILD-TYPE  89 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   14
  22Q GAIN WILD-TYPE   89  366
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 3                 89
  YES               14                366
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           0    15
  22Q GAIN WILD-TYPE                        15   422
D38V7, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          15                422
[1] 4 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, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  13
  22Q GAIN WILD-TYPE  17 406
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   13
  22Q GAIN WILD-TYPE   17  406
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               13                406
[1] 2 2
[1] FALSE

Clustering(39) Variable = XP GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    15   3
  XP GAIN WILD-TYPE 361  91
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18               452 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                3                91 
$`XP GAIN MUTATED`
TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5277 TCGA-DU-A5TT TCGA-DU-A5TW TCGA-E1-5302 
       12.43         7.56        50.86         4.96         5.65        50.14 
TCGA-HT-7688 TCGA-HT-8013 TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7493 TCGA-QH-A6CV 
       31.69        63.55        10.52         0.10        35.90        14.53 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-TM-A84H TCGA-VM-A8C8 TCGA-WY-A859 TCGA-WY-A85E 
       15.06        13.12        30.44        43.04        39.88        20.81 

$`XP GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         8.48         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       46.72        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TY 
       14.17        14.24        12.59        15.12         3.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 
       42.31        23.51         7.50        44.42         0.56        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8015 
       11.28        31.43         1.64        16.24         9.40         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        2.43        15.35        11.05        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        19.33        14.83        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.19         2.04        17.03        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       24.92        16.18        59.05        40.64        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       23.80        15.98        26.99        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        51.06        13.32        43.96        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D 
       46.88        37.71 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.10              0.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            63.55            211.17 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           17.935            18.660 
[1] "0.1 - 63.5 (17.9)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "1"  
D39V2, continuous
D39V3, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    11   7
  XP GAIN WILD-TYPE 195 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     11    7
  XP GAIN WILD-TYPE  195  259
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              11               195
  MALE                 7               259
[1] 2 2
[1] FALSE
D39V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XP GAIN MUTATED            10                5                 3
  XP GAIN WILD-TYPE         166              113               175
D39V5, multiclass
                   clus
vv                  XP GAIN MUTATED XP GAIN WILD-TYPE
  ASTROCYTOMA                    10               166
  OLIGOASTROCYTOMA                5               113
  OLIGODENDROGLIOMA               3               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     5  13
  XP GAIN WILD-TYPE  87 367
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      5   13
  XP GAIN WILD-TYPE   87  367
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                5                87
  YES              13               367
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  0     1
  XP GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                           1    16
  XP GAIN WILD-TYPE                        14   421
D39V7, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         16               421
[1] 4 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, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0  15
  XP GAIN WILD-TYPE  18 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   15
  XP GAIN WILD-TYPE   18  404
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              15               404
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    28   6
  XQ GAIN WILD-TYPE 348  88
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               34               436 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                88 
$`XQ GAIN MUTATED`
TCGA-CS-4938 TCGA-CS-6665 TCGA-DB-5281 TCGA-DU-5871 TCGA-DU-6401 TCGA-DU-6407 
        4.70        12.43        78.28        18.94        87.45        94.52 
TCGA-DU-7007 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-E1-5322 TCGA-FG-A4MY 
       62.96        15.12         4.96         5.65       130.78        23.70 
TCGA-FG-A713 TCGA-HT-7476 TCGA-HT-7609 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7857 
       20.45         6.54        45.99        31.69        14.96         0.23 
TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8563 TCGA-HT-A74J TCGA-HT-A74O TCGA-QH-A65S 
       31.43        63.55        28.27        10.52         0.10         2.53 
TCGA-QH-A6CV TCGA-S9-A6TS TCGA-S9-A7IZ TCGA-S9-A7QX TCGA-TM-A84H TCGA-VV-A86M 
       14.53        62.17         7.13        13.12        30.44        16.01 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85E 
       43.96        39.88        45.80        20.81 

$`XQ GAIN WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        7.69        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       46.72        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        16.83       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96         7.73        11.47       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU 
       16.96        15.48        14.17        14.24        12.59         3.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       78.21        95.57        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J 
       32.61        38.27        10.72        18.38        18.71        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       10.78        36.66        48.69        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       22.06        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        19.23        39.09        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8015 
        3.72        11.28         1.64        16.24         9.40         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.14        16.83        21.40        17.52        17.65         2.43 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       15.35        11.05        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        9.01        13.61        15.16        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.83        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       19.59        30.67        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       22.32        23.51        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       59.05        40.64        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       35.93        23.47        37.05        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D 
       13.32        43.40        46.88        37.71 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.10              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           130.78            211.17 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            20.63             18.61 
[1] "0.1 - 130.8 (20.6)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1.3"
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    23  11
  XQ GAIN WILD-TYPE 183 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     23   11
  XQ GAIN WILD-TYPE  183  255
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              23               183
  MALE                11               255
[1] 2 2
[1] FALSE
D40V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XQ GAIN MUTATED            15               13                 6
  XQ GAIN WILD-TYPE         161              105               172
D40V5, multiclass
                   clus
vv                  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASTROCYTOMA                    15               161
  OLIGOASTROCYTOMA               13               105
  OLIGODENDROGLIOMA               6               172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     8  26
  XQ GAIN WILD-TYPE  84 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8   26
  XQ GAIN WILD-TYPE   84  354
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                8                84
  YES              26               354
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     1
  XQ GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           2    30
  XQ GAIN WILD-TYPE                        13   407
D40V7, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      2                13
  WHITE                                         30               407
[1] 4 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, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3  27
  XQ GAIN WILD-TYPE  15 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   27
  XQ GAIN WILD-TYPE   15  392
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              27               392
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   147  23
  1P LOSS WILD-TYPE 229  71
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              170               300 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               23                71 
$`1P LOSS MUTATED`
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5274 
       64.64         0.10         9.96         8.02         6.61        75.25 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       50.17        44.52        18.84        72.95        31.63        24.20 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
       30.12         5.98        31.40        27.81        29.23        14.40 
TCGA-DB-A75K TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR 
       12.10        31.82         8.02        30.21        17.19        54.25 
TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
       13.12        14.56       182.33        15.16        52.11        22.42 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7018 
       46.06         1.22         7.96       138.28       117.40        30.67 
TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8164 TCGA-DU-8168 
       94.32        62.01        60.30         5.10        21.40        14.17 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 
        8.65         2.70        77.98         5.98        21.30        17.98 
TCGA-DU-A7TG TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       44.42       134.27        78.21        95.57       130.78        75.02 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7638 
       14.33         0.23        47.77        34.36        15.35        22.55 
TCGA-FG-7641 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A60K 
       20.61        14.24        16.01        20.09        22.52        17.82 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 
       15.02        16.44        36.66        20.45         0.10         6.67 
TCGA-HT-7471 TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 
        0.13        24.26        75.19        95.93         4.57         3.16 
TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 
       22.06         0.23        14.27        16.24        44.68         0.10 
TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7874 
        2.96         6.90        14.53        39.09         0.23        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 
        0.33         0.13        35.47         1.64         9.40         6.25 
TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A619 
        5.56        29.59        26.04         0.07        16.93        21.40 
TCGA-HT-A61C TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 
       17.65        15.35        11.05        29.92        19.89        40.18 
TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EX 
        4.31        17.82        20.35        42.77        14.40         1.64 
TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A72Z TCGA-P5-A730 TCGA-QH-A65V TCGA-QH-A65X 
        4.11         0.76        11.64         0.20        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 
       14.04        14.83        14.53         2.20         9.17        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.34        16.73        11.08        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 TCGA-S9-A6TW 
       59.38        30.87         5.46        28.08        30.67        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD 
       34.49        31.33        23.64        32.61       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP 
       72.59        32.45        84.99        31.10        15.91        15.16 
TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY 
       36.13        23.51         8.19         2.04        17.03        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O 
       13.02       169.84        49.32        40.64        24.79        33.24 
TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 
       18.61        14.93        13.51         0.10        35.93        37.05 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        51.06 

$`1P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
       21.01         6.38        17.69        23.84        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        8.48         7.56         7.40       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       72.92        50.86        36.56        78.28        46.42        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64S 
       46.72        39.78        37.45        33.57        25.48        27.45 
TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       18.51        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       30.31        14.40        42.05        27.81        17.19        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.45        18.61        18.02        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 
        8.45         6.81        18.94        17.49       211.17        49.02 
TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       75.16        65.75        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 
       90.77        26.30        10.36         7.96        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       25.91        23.31        41.98         2.76        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
       20.68        19.13        16.96        15.48        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 
       15.12         4.96         3.65         5.65        12.20         7.23 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       11.41        26.76         7.13       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       23.51         7.50         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 
       79.99        57.93        32.45        36.82        32.35         0.20 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       25.48        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8188 
       18.44        17.88        20.09        12.95        13.68        14.96 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 
       14.76        16.41        22.26        28.54        10.78        48.69 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 
       13.58         5.72        27.52        11.54        40.11         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38        40.34 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 
      122.47        17.29        45.99        56.09        57.60         0.16 
TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        0.76         6.05        42.74        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 
        0.10        17.52        39.48        19.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
       23.61         3.68         5.33         3.72        11.28        31.43 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8114 
        0.10         0.46         2.50        13.78         0.23        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA 
       28.27        15.72         0.23         0.13        20.22        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        0.10         5.33         2.70         1.81        16.14        16.83 
TCGA-HT-A61B TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7490 
       17.52         2.43        10.52         0.10         8.32        19.23 
TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL 
       35.90        21.70        21.60        19.59        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY 
       20.71        19.00        14.40         0.23         6.71         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        2.30         5.88         7.63         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A6CS 
       13.25         9.01        13.61        15.16         2.53        19.33 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       13.61        12.23        10.29         1.91        16.50         5.03 
TCGA-QH-A870 TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU 
       12.99         9.90         2.07        19.59        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 
       18.77        28.70        22.95        17.62        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WQ 
       95.93         5.85        80.12        19.86        18.61        14.07 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX 
        7.92        22.32         7.13        20.02        15.06        13.12 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       11.97        49.45        48.33        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        30.44        28.08        24.16        40.83 
TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       25.38        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CD TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 
        7.89        23.47        16.01         8.05        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           182.33            211.17 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           20.220            18.475 
[1] "0.1 - 182.3 (20.2)" "0.0 - 211.2 (18.5)"
[1] "hr=" "2"  
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    76  95
  1P LOSS WILD-TYPE 130 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     76   95
  1P LOSS WILD-TYPE  130  171
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              76               130
  MALE                95               171
[1] 2 2
[1] FALSE
D41V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1P LOSS MUTATED             9               34               128
  1P LOSS WILD-TYPE         167               84                50
D41V5, multiclass
                   clus
vv                  1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASTROCYTOMA                     9               167
  OLIGOASTROCYTOMA               34                84
  OLIGODENDROGLIOMA             128                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    23 148
  1P LOSS WILD-TYPE  69 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     23  148
  1P LOSS WILD-TYPE   69  232
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               23                69
  YES             148               232
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     5
  1P LOSS WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           4   156
  1P LOSS WILD-TYPE                        11   281
D41V7, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          5                 3
  BLACK OR AFRICAN AMERICAN                      4                11
  WHITE                                        156               281
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6 153
  1P LOSS WILD-TYPE  12 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6  153
  1P LOSS WILD-TYPE   12  266
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                12
  NOT HISPANIC OR LATINO             153               266
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    18   6
  1Q LOSS WILD-TYPE 358  88
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               24               446 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                88 
$`1Q LOSS MUTATED`
TCGA-CS-5396 TCGA-DB-5279 TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DU-5849 
        9.96        44.52        31.82         8.02        30.21        14.56 
TCGA-DU-6400 TCGA-DU-7294 TCGA-DU-8158 TCGA-DU-A5TS TCGA-DU-A7TG TCGA-E1-5322 
        1.22        94.32         5.10        15.12        44.42       130.78 
TCGA-FG-5962 TCGA-FG-8185 TCGA-HT-7477 TCGA-HT-7857 TCGA-HT-8113 TCGA-P5-A5F4 
       47.77        14.24        24.26         0.23        29.59         0.76 
TCGA-QH-A65S TCGA-QH-A65Z TCGA-QH-A6CV TCGA-RY-A83Y TCGA-S9-A6WI TCGA-S9-A7R1 
        2.53        14.04        14.53         5.46        84.99       169.84 

$`1Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.86        50.17        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        19.96        30.31 
TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       14.40        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 
       13.12        13.38         3.45        18.61        18.02        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       26.30        10.36         7.96        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       25.91        60.30        23.31        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.17        14.24        12.59         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5302 
       77.88        42.31        23.51         7.50         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
       95.57        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 
       22.55        20.61        20.09        12.95        13.68        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 
        6.90        14.53        39.48        19.23        39.09        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       13.78         0.23        34.19        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       21.40        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 
        2.37         2.30         4.11         5.88         7.63         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU 
       13.61        15.16        12.62        15.85        19.33        14.83 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       28.37        13.02        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.23              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           169.84            211.17 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            14.84             18.71 
[1] "0.2 - 169.8 (14.8)" "0.0 - 211.2 (18.7)"
[1] "hr=" "1.1"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    11  13
  1Q LOSS WILD-TYPE 195 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   13
  1Q LOSS WILD-TYPE  195  253
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11               195
  MALE                13               253
[1] 2 2
[1] FALSE
D42V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1Q LOSS MUTATED             4                4                16
  1Q LOSS WILD-TYPE         172              114               162
D42V5, multiclass
                   clus
vv                  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASTROCYTOMA                     4               172
  OLIGOASTROCYTOMA                4               114
  OLIGODENDROGLIOMA              16               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     6  18
  1Q LOSS WILD-TYPE  86 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6   18
  1Q LOSS WILD-TYPE   86  362
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                6                86
  YES              18               362
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           2    20
  1Q LOSS WILD-TYPE                        13   417
D42V7, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      2                13
  WHITE                                         20               417
[1] 4 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, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  22
  1Q LOSS WILD-TYPE  17 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   22
  1Q LOSS WILD-TYPE   17  397
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              22               397
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    14   5
  2P LOSS WILD-TYPE 362  89
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               19               451 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5                89 
$`2P LOSS MUTATED`
TCGA-CS-6186 TCGA-CS-6666 TCGA-DH-5142 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-A7T6 
       17.69         8.48        30.31        14.99       117.40        17.98 
TCGA-FG-A6J3 TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-A5R7 
       22.26        11.54        24.26         0.10         2.96        20.22 
TCGA-HT-A61B TCGA-HW-7493 TCGA-P5-A5F6 TCGA-P5-A733 TCGA-QH-A6CW TCGA-S9-A89V 
       17.52        35.90         1.28        13.61        13.61        18.71 
TCGA-VM-A8C8 
       43.04 

$`2P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6188 
       40.18         0.10        21.01         9.96         6.38        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       26.76         7.13        21.30       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       31.69        14.96         0.10        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59        34.19        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04         0.13         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        5.88         7.63         0.76         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
       11.64         0.20         9.01        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX 
       15.85        14.04        19.33        14.83        14.53        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        31.59        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.10              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           117.40            211.17 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            17.69             18.77 
[1] "0.1 - 117.4 (17.7)" "0.0 - 211.2 (18.8)"
[1] "hr=" "1.8"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7  12
  2P LOSS WILD-TYPE 199 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7   12
  2P LOSS WILD-TYPE  199  254
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               199
  MALE                12               254
[1] 2 2
[1] FALSE
D43V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2P LOSS MUTATED            10                4                 5
  2P LOSS WILD-TYPE         166              114               173
D43V5, multiclass
                   clus
vv                  2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASTROCYTOMA                    10               166
  OLIGOASTROCYTOMA                4               114
  OLIGODENDROGLIOMA               5               173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3  16
  2P LOSS WILD-TYPE  89 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   16
  2P LOSS WILD-TYPE   89  364
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                3                89
  YES              16               364
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           0    19
  2P LOSS WILD-TYPE                        15   418
D43V7, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         19               418
[1] 4 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, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  18
  2P LOSS WILD-TYPE  18 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   18
  2P LOSS WILD-TYPE   18  401
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              18               401
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    13   3
  2Q LOSS WILD-TYPE 363  91
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               454 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                91 
$`2Q LOSS MUTATED`
TCGA-CS-6666 TCGA-DB-5277 TCGA-DH-5142 TCGA-DH-A66B TCGA-DU-6408 TCGA-DU-A7T6 
        8.48        50.86        30.31        42.05       114.08        17.98 
TCGA-FG-A6J3 TCGA-HT-7477 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-A618 TCGA-HT-A61B 
       22.26        24.26         0.10         2.96        16.83        17.52 
TCGA-HW-7493 TCGA-P5-A5F6 TCGA-P5-A733 TCGA-QH-A6CW 
       35.90         1.28        13.61        13.61 

$`2Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95        12.43         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       14.40         8.02        30.21        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        13.12        13.38         3.45        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
       94.52         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       26.76         7.13        21.30       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 
        0.10        31.69        14.96         0.10        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       21.40        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         5.88         7.63         0.76         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65S 
       13.25        11.64         0.20         9.01        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.10              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           114.08            211.17 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            17.75             18.71 
[1] "0.1 - 114.1 (17.8)" "0.0 - 211.2 (18.7)"
[1] "hr=" "1.1"
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     6  10
  2Q LOSS WILD-TYPE 200 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      6   10
  2Q LOSS WILD-TYPE  200  256
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               6               200
  MALE                10               256
[1] 2 2
[1] FALSE
D44V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2Q LOSS MUTATED            10                3                 3
  2Q LOSS WILD-TYPE         166              115               175
D44V5, multiclass
                   clus
vv                  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASTROCYTOMA                    10               166
  OLIGOASTROCYTOMA                3               115
  OLIGODENDROGLIOMA               3               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     3  13
  2Q LOSS WILD-TYPE  89 367
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3   13
  2Q LOSS WILD-TYPE   89  367
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                3                89
  YES              13               367
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     0
  2Q LOSS WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           0    16
  2Q LOSS WILD-TYPE                        15   421
D44V7, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         16               421
[1] 4 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, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  16
  2Q LOSS WILD-TYPE  18 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   16
  2Q LOSS WILD-TYPE   18  403
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              16               403
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    16   9
  3P LOSS WILD-TYPE 360  85
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               25               445 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                85 
$`3P LOSS MUTATED`
TCGA-CS-6666 TCGA-DB-5277 TCGA-DH-A66D TCGA-DU-6396 TCGA-DU-7300 TCGA-DU-A5TU 
        8.48        50.86        27.81        75.16        62.01         3.65 
TCGA-DU-A76R TCGA-DU-A7TA TCGA-E1-A7YV TCGA-E1-A7YW TCGA-HT-7469 TCGA-HT-7477 
       21.30        77.88        32.45        36.82        11.54        24.26 
TCGA-HT-7690 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A5RA TCGA-HT-A619 TCGA-IK-7675 
        0.10         0.23        15.72        27.35        21.40        19.00 
TCGA-P5-A5F6 TCGA-S9-A89V TCGA-TM-A84B TCGA-TM-A84J TCGA-TQ-A7RH TCGA-VM-A8C8 
        1.28        18.71        24.92        24.16        15.98        43.04 
TCGA-VV-A829 
       37.05 

$`3P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95        12.43         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F 
       30.31        14.40         8.02        30.21        42.05        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       52.11        22.42        49.02        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        44.02        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59        15.12         4.96         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
        7.13        17.98       124.50        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
       13.58         5.72        27.52         0.10         6.67        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         5.56        13.78        29.59        34.19 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       28.27         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.83        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        20.35        12.76        20.81        20.71        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U 
        2.30         4.11         5.88         7.63         0.76         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L 
       16.18        59.05        40.64        30.44        28.08        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RW TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       26.99        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       23.47        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.10              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            77.88            211.17 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            24.16             18.44 
[1] "0.1 - 77.9 (24.2)"  "0.0 - 211.2 (18.4)"
[1] "hr=" "2.1"
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     8  18
  3P LOSS WILD-TYPE 198 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      8   18
  3P LOSS WILD-TYPE  198  248
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               8               198
  MALE                18               248
[1] 2 2
[1] FALSE
D45V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3P LOSS MUTATED            10                7                 9
  3P LOSS WILD-TYPE         166              111               169
D45V5, multiclass
                   clus
vv                  3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASTROCYTOMA                    10               166
  OLIGOASTROCYTOMA                7               111
  OLIGODENDROGLIOMA               9               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     4  22
  3P LOSS WILD-TYPE  88 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4   22
  3P LOSS WILD-TYPE   88  358
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                4                88
  YES              22               358
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     1
  3P LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           0    24
  3P LOSS WILD-TYPE                        15   413
D45V7, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         24               413
[1] 4 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, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     3  22
  3P LOSS WILD-TYPE  15 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3   22
  3P LOSS WILD-TYPE   15  397
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              22               397
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    13  12
  3Q LOSS WILD-TYPE 363  82
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               25               445 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12                82 
$`3Q LOSS MUTATED`
TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5281 TCGA-DU-6396 TCGA-DU-7007 TCGA-DU-7014 
        8.48        50.86        78.28        75.16        62.96       117.40 
TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-8167 TCGA-DU-A5TU TCGA-DU-A76R TCGA-E1-5302 
       18.94        62.01        15.48         3.65        21.30        50.14 
TCGA-E1-A7YV TCGA-HT-7469 TCGA-HT-7472 TCGA-HT-7477 TCGA-HT-8111 TCGA-HT-8564 
       32.45        11.54         0.03        24.26         0.23        15.72 
TCGA-HT-A619 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-S9-A6TV TCGA-TM-A84B TCGA-TM-A84J 
       21.40        19.00         1.28        18.77        24.92        24.16 
TCGA-VM-A8C8 
       43.04 

$`3Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95        12.43         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       46.72        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       52.11        22.42        49.02        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      138.28        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 
       30.67        26.30        10.36         7.96        94.32        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         4.96         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76         7.13        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 
       42.31        23.51         7.50        44.42         0.56        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      130.78        75.02        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 
        0.10         6.67        40.11         0.13        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV 
       13.78        29.59        34.19        28.27         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B 
        2.70        16.93         1.81        16.14        16.83        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        20.81        20.71        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        5.88         7.63         0.76         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       62.17        87.12        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       48.33        49.32        34.78        48.39        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       40.64        30.44        28.08        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.03              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           117.40            211.17 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            21.40             18.44 
[1] "0.0 - 117.4 (21.4)" "0.1 - 211.2 (18.4)"
[1] "hr=" "2.2"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     8  17
  3Q LOSS WILD-TYPE 198 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      8   17
  3Q LOSS WILD-TYPE  198  249
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               8               198
  MALE                17               249
[1] 2 2
[1] FALSE
D46V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3Q LOSS MUTATED             9                6                10
  3Q LOSS WILD-TYPE         167              112               168
D46V5, multiclass
                   clus
vv                  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASTROCYTOMA                     9               167
  OLIGOASTROCYTOMA                6               112
  OLIGODENDROGLIOMA              10               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     6  19
  3Q LOSS WILD-TYPE  86 361
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6   19
  3Q LOSS WILD-TYPE   86  361
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                6                86
  YES              19               361
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     1
  3Q LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           1    23
  3Q LOSS WILD-TYPE                        14   414
D46V7, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         23               414
[1] 4 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, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2  22
  3Q LOSS WILD-TYPE  16 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   22
  3Q LOSS WILD-TYPE   16  397
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                16
  NOT HISPANIC OR LATINO              22               397
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    50  13
  4P LOSS WILD-TYPE 326  81
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               63               407 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               13                81 
$`4P LOSS MUTATED`
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XH 
       75.25        47.93        50.86        44.52        18.84        31.63 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-A669 TCGA-DH-A66G TCGA-DH-A7UT TCGA-DU-6399 
       14.40        18.51        30.21        17.19        13.38        65.75 
TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8165 
        1.22         7.96        14.99        30.67        94.32        19.13 
TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A6S3 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T8 
       16.96        14.17         2.70         5.98        21.30       124.50 
TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5311 TCGA-F6-A8O3 
       77.88        50.14        67.46        41.13       134.27         0.23 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-A60J TCGA-FG-A6IZ 
       47.77        34.36        17.88        22.55        14.76        15.02 
TCGA-FG-A6J1 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7480 
       16.44         0.10         6.67         0.13        17.42        75.19 
TCGA-HT-7677 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-8105 TCGA-HT-A5R9 TCGA-HT-A619 
       16.24        31.69         2.96         6.25         0.07        21.40 
TCGA-HT-A74K TCGA-HW-7487 TCGA-HW-7491 TCGA-IK-8125 TCGA-P5-A5EV TCGA-S9-A6TW 
       15.35        19.89        40.18        42.77         0.23        37.84 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WL TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-TM-A7C5 
      106.39        69.50        31.10        23.51         7.13        49.32 
TCGA-TM-A84T TCGA-TQ-A7RW TCGA-WH-A86K 
       23.80        26.99        13.32 

$`4P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-5278 
        7.40         6.61       122.73        81.96        72.92        50.17 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        78.28        46.42        30.21        46.72        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       37.45        33.57        72.95        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A75K 
        5.98        31.40        27.45        27.81        29.23        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        42.05        27.81        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       54.25        13.12         3.45        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       49.02        75.16        46.06        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 
      133.74        19.89        16.83        94.52       114.08         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84       117.40        90.77        26.30        10.36         7.96 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       21.40        15.48        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 
        3.65         5.65        12.20         8.65        77.98         7.23 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC 
       11.41        26.76         7.13        17.98        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 
        7.50        44.42         0.56        79.99        57.93        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       14.33         0.20        25.48        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 
       24.99        23.97        18.44        15.35        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       23.70        17.82        16.41        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 
       11.54        40.11         0.03        16.54         3.75         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       24.26         6.38        40.34        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
        0.23        14.27         0.16         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 
       42.74         0.10        14.96         0.10         0.10        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        26.04         0.13        20.22        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74L TCGA-HT-A74O 
       17.52        17.65         2.43        10.52        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       29.92         8.32        19.23        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        14.40        14.40         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH TCGA-VM-A8C8 TCGA-VM-A8C9 
       25.38        18.61        14.93        15.98        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21         8.05        51.06        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.07              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           134.27            211.17 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            21.30             18.44 
[1] "0.1 - 134.3 (21.3)" "0.0 - 211.2 (18.4)"
[1] "hr=" "1.1"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    21  42
  4P LOSS WILD-TYPE 185 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     21   42
  4P LOSS WILD-TYPE  185  224
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              21               185
  MALE                42               224
[1] 2 2
[1] FALSE
D47V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4P LOSS MUTATED            12               14                37
  4P LOSS WILD-TYPE         164              104               141
D47V5, multiclass
                   clus
vv                  4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASTROCYTOMA                    12               164
  OLIGOASTROCYTOMA               14               104
  OLIGODENDROGLIOMA              37               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"
D47V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    16  47
  4P LOSS WILD-TYPE  76 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     16   47
  4P LOSS WILD-TYPE   76  333
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               16                76
  YES              47               333
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           0    60
  4P LOSS WILD-TYPE                        15   377
D47V7, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 6
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         60               377
[1] 4 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, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  60
  4P LOSS WILD-TYPE  17 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   60
  4P LOSS WILD-TYPE   17  359
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              60               359
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    66  16
  4Q LOSS WILD-TYPE 310  78
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               82               388 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16                78 
$`4Q LOSS MUTATED`
TCGA-CS-4943 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XA 
       18.15        75.25        47.93        50.86        44.52        18.84 
TCGA-DB-A4XE TCGA-DB-A4XH TCGA-DB-A64W TCGA-DB-A75O TCGA-DH-A669 TCGA-DH-A66B 
       37.45        31.63        14.40        30.74        30.21        42.05 
TCGA-DH-A66G TCGA-DU-5853 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7008 
       17.19        13.38        65.75         1.22         7.96       156.23 
TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-7309 
       14.99        30.67        94.32        44.02        60.30         2.76 
TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S3 TCGA-DU-A6S8 TCGA-DU-A76R 
       19.13        14.17        15.12         2.70         5.98        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5311 
      124.50        77.88        50.14        67.46        41.13       134.27 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-7636 
       14.33         0.23        47.77        25.48        34.36        17.88 
TCGA-FG-7638 TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-HT-7467 TCGA-HT-7468 
       22.55        14.76        15.02        16.44         0.10         6.67 
TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7677 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7856 
        0.13        75.19        16.24        31.69         2.96        39.09 
TCGA-HT-8105 TCGA-HT-A5R9 TCGA-HT-A619 TCGA-HT-A74K TCGA-HW-7487 TCGA-HW-7491 
        6.25         0.07        21.40        15.35        19.89        40.18 
TCGA-HW-7493 TCGA-IK-8125 TCGA-P5-A5EV TCGA-QH-A6X4 TCGA-QH-A6XA TCGA-S9-A6TW 
       35.90        42.77         0.23        14.53        16.50        37.84 
TCGA-S9-A6WD TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ 
       69.50        31.10        15.16         7.92        23.51         7.13 
TCGA-S9-A7J0 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A84R TCGA-TM-A84T TCGA-TQ-A7RW 
       20.02        48.33        49.32        18.61        23.80        26.99 
TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85E 
       13.32        39.88        43.40        20.81 

$`4Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 
        6.61       122.73        81.96        72.92        50.17        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF 
       78.28        46.42        30.21        46.72        39.78        33.57 
TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.45        27.81        29.23        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       17.88        16.18        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
        8.02        27.81        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7009 
       94.52       114.08         7.73        11.47        62.96       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 
      105.21         6.54         8.84       117.40        90.77        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7304 
       10.36         7.96        18.94        62.01        25.91        23.31 
TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       16.96        15.48        14.24        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K 
        5.65        12.20         8.65        77.98         7.23        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       26.76         7.13        17.98        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 
       44.42         0.56        79.99        57.93        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 
      130.78        75.02        32.45        36.82        32.35         0.20 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       15.35        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L 
       10.72        18.38        18.71        23.70        17.82        16.41 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 
       13.58         5.72        27.52        11.54        40.11         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       40.34        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
        0.16         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         0.10        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        19.23         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 
       63.55         0.10        37.87        33.01        12.23         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       20.22        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
        1.81        16.14        16.83        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7489 TCGA-HW-7490 
       10.52        11.05         0.10        29.92         8.32        19.23 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        20.81        20.71        19.00        14.40        14.40 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X5 
       13.61        12.23         2.20         9.17        10.29        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
       16.73         1.91         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM 
      106.39        72.59        80.12        32.45        84.99        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7J1 
       15.91        18.61        14.07        36.13        22.32         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       18.71        11.97        49.45        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-TQ-A7RH 
       40.83        24.79        33.24        25.38        14.93        15.98 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WY-A858 TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        45.80        46.88        37.71 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.07              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           156.23            211.17 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           21.975            17.965 
[1] "0.1 - 156.2 (22.0)" "0.0 - 211.2 (18.0)"
[1] "hr=" "1.2"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    31  51
  4Q LOSS WILD-TYPE 175 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     31   51
  4Q LOSS WILD-TYPE  175  215
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              31               175
  MALE                51               215
[1] 2 2
[1] FALSE
D48V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4Q LOSS MUTATED            20               18                44
  4Q LOSS WILD-TYPE         156              100               134
D48V5, multiclass
                   clus
vv                  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASTROCYTOMA                    20               156
  OLIGOASTROCYTOMA               18               100
  OLIGODENDROGLIOMA              44               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"
D48V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    19  63
  4Q LOSS WILD-TYPE  73 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     19   63
  4Q LOSS WILD-TYPE   73  317
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               19                73
  YES              63               317
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           1    78
  4Q LOSS WILD-TYPE                        14   359
D48V7, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 6
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         78               359
[1] 4 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, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     1  75
  4Q LOSS WILD-TYPE  17 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   75
  4Q LOSS WILD-TYPE   17  344
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              75               344
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    26   7
  5P LOSS WILD-TYPE 350  87
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               33               437 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                87 
$`5P LOSS MUTATED`
TCGA-CS-4943 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4XE 
       18.15        47.93        72.92        50.86        78.28        37.45 
TCGA-DB-A4XH TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-6399 
       31.63        18.51        19.96        27.81        17.19        65.75 
TCGA-DU-7007 TCGA-DU-7306 TCGA-DU-8165 TCGA-DU-A7T6 TCGA-E1-5302 TCGA-FG-5965 
       62.96        41.98        19.13        17.98        50.14        36.82 
TCGA-FG-6689 TCGA-FG-A6J3 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7688 TCGA-HT-7884 
       14.93        22.26         3.75        17.42        31.69        11.28 
TCGA-HT-8106 TCGA-HT-A614 TCGA-HT-A61B TCGA-P5-A72W TCGA-RY-A83Z TCGA-S9-A6WM 
        0.10         2.70        17.52        10.42         9.90        19.86 
TCGA-S9-A7R7 TCGA-TM-A84I TCGA-WY-A859 
       98.63        28.08        39.88 

$`5P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5278 TCGA-DB-5279 
        6.61       122.73        81.96        75.25        50.17        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        46.42        18.84        30.21        46.72        39.78 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        14.40        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A7UR 
       14.40         8.02        30.21        42.05        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       13.12        13.38         3.45        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        46.06         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96         7.73        11.47       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 
       62.01        25.91        60.30        23.31         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       18.77        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       16.41        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
       35.47         3.72        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 
       20.22         0.07        27.35         0.10         5.33        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H 
        1.81        16.14        16.83        21.40        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z 
        7.63         0.76         1.28         0.16        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 
       13.02       169.84        10.39        99.06        30.05        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.10              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            98.63            211.17 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            22.26             18.44 
[1] "0.1 - 98.6 (22.3)"  "0.0 - 211.2 (18.4)"
[1] "hr=" "1"  
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    14  19
  5P LOSS WILD-TYPE 192 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     14   19
  5P LOSS WILD-TYPE  192  247
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              14               192
  MALE                19               247
[1] 2 2
[1] FALSE
D49V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5P LOSS MUTATED            17               11                 5
  5P LOSS WILD-TYPE         159              107               173
D49V5, multiclass
                   clus
vv                  5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASTROCYTOMA                    17               159
  OLIGOASTROCYTOMA               11               107
  OLIGODENDROGLIOMA               5               173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    12  21
  5P LOSS WILD-TYPE  80 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     12   21
  5P LOSS WILD-TYPE   80  359
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               12                80
  YES              21               359
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           0    33
  5P LOSS WILD-TYPE                        15   404
D49V7, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         33               404
[1] 4 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, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  31
  5P LOSS WILD-TYPE  18 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   31
  5P LOSS WILD-TYPE   18  388
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              31               388
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    21  12
  5Q LOSS WILD-TYPE 355  82
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               437 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               12                82 
$`5Q LOSS MUTATED`
TCGA-CS-6665 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4XH TCGA-DB-A64X 
       12.43        72.92        50.86        78.28        31.63        18.51 
TCGA-DH-5140 TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6408 
       19.96        27.81        17.19        65.75        87.45       114.08 
TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-8165 TCGA-DU-A7T6 TCGA-E1-5302 TCGA-E1-5304 
       62.96        14.99        19.13        17.98        50.14        41.13 
TCGA-FG-A6J3 TCGA-HT-7477 TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-8106 TCGA-HT-A614 
       22.26        24.26         3.68        11.28         0.10         2.70 
TCGA-HT-A618 TCGA-HT-A61B TCGA-IK-7675 TCGA-P5-A72W TCGA-S9-A6TS TCGA-S9-A6WM 
       16.83        17.52        19.00        10.42        62.17        19.86 
TCGA-TM-A84I TCGA-WH-A86K TCGA-WY-A859 
       28.08        13.32        39.88 

$`5Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5278 
        6.61       122.73        81.96        75.25        47.93        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        36.56        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O 
       39.78        37.45        33.57        72.95        24.20        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       14.40        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 
       52.11        22.42        49.02        75.16        46.06         1.22 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.96         7.73        11.47       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 
        0.13         5.33        35.47         3.72        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         6.25         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59        34.19        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61C 
        5.33        16.93         1.81        16.14        21.40        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.81        20.71        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z 
        7.63         0.76         1.28         0.16        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU 
        9.90        28.08         2.07        19.59        30.67        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 
       37.05        16.01        23.21         8.05        51.06        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           114.08            211.17 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            19.96             18.44 
[1] "0.1 - 114.1 (20.0)" "0.0 - 211.2 (18.4)"
[1] "hr=" "1.6"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    17  16
  5Q LOSS WILD-TYPE 189 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     17   16
  5Q LOSS WILD-TYPE  189  250
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              17               189
  MALE                16               250
[1] 2 2
[1] FALSE
D50V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5Q LOSS MUTATED            20                6                 7
  5Q LOSS WILD-TYPE         156              112               171
D50V5, multiclass
                   clus
vv                  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASTROCYTOMA                    20               156
  OLIGOASTROCYTOMA                6               112
  OLIGODENDROGLIOMA               7               171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    11  22
  5Q LOSS WILD-TYPE  81 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11   22
  5Q LOSS WILD-TYPE   81  358
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               11                81
  YES              22               358
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     0
  5Q LOSS WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           0    33
  5Q LOSS WILD-TYPE                        15   404
D50V7, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         33               404
[1] 4 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, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1  31
  5Q LOSS WILD-TYPE  17 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   31
  5Q LOSS WILD-TYPE   17  388
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              31               388
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    15  11
  6P LOSS WILD-TYPE 361  83
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               26               444 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11                83 
$`6P LOSS MUTATED`
TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64O 
        6.38         8.48        50.86        33.57        31.63        25.48 
TCGA-DH-A669 TCGA-DU-6400 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-A7T6 TCGA-FG-5963 
       30.21         1.22         5.10        23.74        17.98        25.48 
TCGA-FG-8191 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A617 
       32.61         2.96        19.23        15.72         0.23        16.14 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-QH-A6CX TCGA-S9-A6TZ TCGA-TM-A7CF 
        0.76         1.28        19.33        12.23        28.70        48.39 
TCGA-VM-A8C8 TCGA-VM-A8CD 
       43.04         7.89 

$`6P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         9.96        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P 
       46.72        39.78        37.45        72.95        24.20        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 
       25.91        60.30        23.31        41.98         2.76        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76         7.13        21.30       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 
       14.33         0.23         0.20        47.77        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT 
       14.24        16.01        20.09        14.96        22.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 
        5.33         2.70        16.93         1.81        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A72U TCGA-P5-A72W 
        2.30         4.11         5.88         7.63         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        15.85        14.04        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       13.61         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 
       87.12        18.77        37.84        34.49        31.33        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08        13.51         0.10        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.23              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            50.86            211.17 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           18.605            18.660 
[1] "0.2 - 50.9 (18.6)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "3.9"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    12  14
  6P LOSS WILD-TYPE 194 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     12   14
  6P LOSS WILD-TYPE  194  252
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              12               194
  MALE                14               252
[1] 2 2
[1] FALSE
D51V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6P LOSS MUTATED            14                4                 8
  6P LOSS WILD-TYPE         162              114               170
D51V5, multiclass
                   clus
vv                  6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASTROCYTOMA                    14               162
  OLIGOASTROCYTOMA                4               114
  OLIGODENDROGLIOMA               8               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  21
  6P LOSS WILD-TYPE  87 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   21
  6P LOSS WILD-TYPE   87  359
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                5                87
  YES              21               359
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  1     0
  6P LOSS WILD-TYPE                                0     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           0    25
  6P LOSS WILD-TYPE                        15   412
D51V7, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         25               412
[1] 4 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, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  22
  6P LOSS WILD-TYPE  17 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   22
  6P LOSS WILD-TYPE   17  397
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              22               397
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    38  16
  6Q LOSS WILD-TYPE 338  78
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               54               416 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16                78 
$`6Q LOSS MUTATED`
TCGA-CS-4944 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5280 TCGA-DB-A4XF TCGA-DB-A4XH 
       10.62         6.38         8.48        36.56        33.57        31.63 
TCGA-DB-A64O TCGA-DH-A669 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5855 TCGA-DU-5872 
       25.48        30.21        42.05        18.02         6.81        17.49 
TCGA-DU-6400 TCGA-DU-6405 TCGA-DU-6542 TCGA-DU-7012 TCGA-DU-7298 TCGA-DU-8158 
        1.22        19.89         7.73         6.54        18.94         5.10 
TCGA-DU-8161 TCGA-DU-A7T6 TCGA-DU-A7TC TCGA-E1-5307 TCGA-FG-5963 TCGA-FG-7636 
       23.74        17.98        23.51        57.93        25.48        17.88 
TCGA-FG-8191 TCGA-FG-A6J3 TCGA-HT-7475 TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7689 
       32.61        22.26        17.42        17.29        31.69        14.96 
TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RB TCGA-HT-A617 
        2.96        19.23        15.72         0.23         0.10        16.14 
TCGA-HT-A619 TCGA-HW-A5KK TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F4 
       21.40        12.76         0.23         2.30         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72W TCGA-QH-A6CS TCGA-QH-A6CX TCGA-QH-A870 TCGA-S9-A6TZ 
        1.28        10.42        19.33        12.23        12.99        28.70 
TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8CD TCGA-WY-A85B 
       31.59        48.39        25.38        43.04         7.89        45.80 

$`6Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10        21.01         9.96        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       12.43         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
       81.96        75.25        47.93        72.92        50.86        50.17 
TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       39.78        37.45        72.95        24.20        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F 
       31.82        30.31        14.40         8.02        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 
       14.56        17.46         6.74        13.38         8.45       182.33 
TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
      133.74        16.83        94.52       114.08         7.96        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 
       62.96       156.23       138.28        14.99       105.21         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
       41.98         2.76        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG 
       21.30       124.50        77.88        42.31         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 
        0.56        50.14        67.46        41.13        79.99       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 
       32.35        14.33         0.23         0.20        47.77        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       15.35        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT 
       14.24        16.01        20.09        14.96        22.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       16.41        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18       122.47         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 
        0.76        44.68         6.05        42.74         0.10         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        0.10        17.52         6.90        14.53        39.48        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
       28.27        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B 
        5.33         2.70        16.93         1.81        16.83        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72U 
        6.71         1.64         2.37         4.11         5.88         0.16 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        15.85        14.04        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       13.61         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK 
       16.73         1.91        16.50         5.03        11.08        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        37.84        34.49        31.33        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       24.16        40.83        24.79        33.24        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       23.80        15.98        26.99        30.08        13.51         0.10 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85C 
       51.06        13.32        43.96        39.88        43.40        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.10              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            57.93            211.17 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           17.685            18.770 
[1] "0.1 - 57.9 (17.7)"  "0.0 - 211.2 (18.8)"
[1] "hr=" "3.1"
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    26  29
  6Q LOSS WILD-TYPE 180 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     26   29
  6Q LOSS WILD-TYPE  180  237
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              26               180
  MALE                29               237
[1] 2 2
[1] FALSE
D52V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6Q LOSS MUTATED            34               10                11
  6Q LOSS WILD-TYPE         142              108               167
D52V5, multiclass
                   clus
vv                  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASTROCYTOMA                    34               142
  OLIGOASTROCYTOMA               10               108
  OLIGODENDROGLIOMA              11               167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    15  40
  6Q LOSS WILD-TYPE  77 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15   40
  6Q LOSS WILD-TYPE   77  340
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               15                77
  YES              40               340
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  1     1
  6Q LOSS WILD-TYPE                                0     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    50
  6Q LOSS WILD-TYPE                        12   387
D52V7, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      3                12
  WHITE                                         50               387
[1] 4 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, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     2  47
  6Q LOSS WILD-TYPE  16 372
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   47
  6Q LOSS WILD-TYPE   16  372
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                16
  NOT HISPANIC OR LATINO              47               372
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     2   1
  7P LOSS WILD-TYPE 374  93
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               467 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                93 
$`7P LOSS MUTATED`
TCGA-HW-A5KL TCGA-P5-A5F6 TCGA-S9-A6TS 
       20.81         1.28        62.17 

$`7P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       20.35        12.76        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         5.88         7.63         0.76         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1.28              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            62.17            211.17 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            20.81             18.61 
[1] "1.3 - 62.2 (20.8)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.7"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   1
  7P LOSS WILD-TYPE 204 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    1
  7P LOSS WILD-TYPE  204  265
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               2               204
  MALE                 1               265
[1] 2 2
[1] FALSE
D53V4, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               267 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5395 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666        TCGA-CS-6667 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-DB-5274        TCGA-DB-A4XE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64L        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A75L        TCGA-DB-A75O        TCGA-DH-5140        TCGA-DH-5142 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-5143        TCGA-DH-5144        TCGA-DH-A66B        TCGA-DH-A66D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7UU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A7UV        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5874        TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7011        TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7018        TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7299        TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7304        TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8161        TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TS        TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A6S2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A6S6        TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7T6        TCGA-DU-A7T8        TCGA-DU-A7TA        TCGA-DU-A7TB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7TC        TCGA-DU-A7TD        TCGA-DU-A7TG        TCGA-E1-5302 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5311        TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YO        TCGA-E1-A7YV        TCGA-E1-A7YW        TCGA-E1-A7Z6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-5963        TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8181        TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-A4MT        TCGA-FG-A4MW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A4MX        TCGA-FG-A60J        TCGA-FG-A60L        TCGA-FG-A6J1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A6J3        TCGA-FG-A711        TCGA-FG-A713        TCGA-FG-A87Q 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7468        TCGA-HT-7470        TCGA-HT-7475        TCGA-HT-7477 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7485        TCGA-HT-7607        TCGA-HT-7609        TCGA-HT-7611 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7689        TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7854        TCGA-HT-7875        TCGA-HT-7884        TCGA-HT-8564 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A4DV        TCGA-HT-A5R7        TCGA-HT-A5RA        TCGA-HT-A5RC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A615        TCGA-HT-A617        TCGA-HT-A618        TCGA-HT-A61B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A61C        TCGA-HT-A74L        TCGA-IK-7675        TCGA-KT-A74X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-KT-A7W1        TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5EX        TCGA-P5-A5F0        TCGA-P5-A5F2        TCGA-P5-A5F4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A731        TCGA-QH-A65R        TCGA-QH-A65S        TCGA-QH-A65V 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A65X        TCGA-QH-A65Z        TCGA-QH-A6CS        TCGA-QH-A6CU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CV        TCGA-QH-A6CW        TCGA-QH-A6CX        TCGA-QH-A6CY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CZ        TCGA-QH-A6X3        TCGA-QH-A6X4        TCGA-QH-A6X5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6X8        TCGA-QH-A6X9        TCGA-QH-A6XA        TCGA-QH-A6XC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A86X        TCGA-QH-A870        TCGA-RY-A83Y        TCGA-RY-A840 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-RY-A845        TCGA-RY-A847        TCGA-S9-A6TU        TCGA-S9-A6TV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6TW        TCGA-S9-A6TX        TCGA-S9-A6TY        TCGA-S9-A6TZ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U0        TCGA-S9-A6U1        TCGA-S9-A6U2        TCGA-S9-A6U5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U6        TCGA-S9-A6U8        TCGA-S9-A6UA        TCGA-S9-A6UB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WD        TCGA-S9-A6WE        TCGA-S9-A6WG        TCGA-S9-A6WH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WI        TCGA-S9-A6WL        TCGA-S9-A6WM        TCGA-S9-A6WN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WO        TCGA-S9-A6WP        TCGA-S9-A6WQ        TCGA-S9-A7IQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7IS        TCGA-S9-A7IX        TCGA-S9-A7IY        TCGA-S9-A7IZ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7J0        TCGA-S9-A7J1        TCGA-S9-A7J2        TCGA-S9-A7J3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7QW        TCGA-S9-A7QX        TCGA-S9-A7QY        TCGA-S9-A7QZ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7R1        TCGA-S9-A7R2        TCGA-S9-A7R3        TCGA-S9-A7R4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7R7        TCGA-S9-A7R8        TCGA-S9-A89V        TCGA-S9-A89Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A7C3        TCGA-TM-A7C4        TCGA-TM-A7C5        TCGA-TM-A7CA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A7CF        TCGA-TM-A84B        TCGA-TM-A84C        TCGA-TM-A84F 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84G        TCGA-TM-A84H        TCGA-TM-A84I        TCGA-TM-A84J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84L        TCGA-TM-A84M        TCGA-TM-A84O        TCGA-TM-A84Q 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TM-A84T        TCGA-TQ-A7RW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8C8        TCGA-VM-A8CA        TCGA-VM-A8CD        TCGA-VM-A8CE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CH        TCGA-WY-A858        TCGA-WY-A859 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7P LOSS MUTATED             2                0                 1
  7P LOSS WILD-TYPE         174              118               177
D53V5, multiclass
                   clus
vv                  7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASTROCYTOMA                     2               174
  OLIGOASTROCYTOMA                0               118
  OLIGODENDROGLIOMA               1               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   3
  7P LOSS WILD-TYPE  92 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE   92  377
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                92
  YES               3               377
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     0
  7P LOSS WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           0     3
  7P LOSS WILD-TYPE                        15   434
D53V7, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          3               434
[1] 4 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, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   2
  7P LOSS WILD-TYPE  18 417
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE   18  417
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               2               417
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     2   1
  7Q LOSS WILD-TYPE 374  93
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               467 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                93 
$`7Q LOSS MUTATED`
TCGA-DH-A66B TCGA-P5-A5F6 TCGA-S9-A6TS 
       42.05         1.28        62.17 

$`7Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         5.88         7.63         0.76         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1.28              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            62.17            211.17 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            42.05             18.61 
[1] "1.3 - 62.2 (42.0)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.3"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   2
  7Q LOSS WILD-TYPE 205 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    2
  7Q LOSS WILD-TYPE  205  264
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               1               205
  MALE                 2               264
[1] 2 2
[1] FALSE
D54V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7Q LOSS MUTATED             2                0                 1
  7Q LOSS WILD-TYPE         174              118               177
D54V5, multiclass
                   clus
vv                  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASTROCYTOMA                     2               174
  OLIGOASTROCYTOMA                0               118
  OLIGODENDROGLIOMA               1               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   3
  7Q LOSS WILD-TYPE  92 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE   92  377
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                92
  YES               3               377
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           0     3
  7Q LOSS WILD-TYPE                        15   434
D54V7, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          3               434
[1] 4 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, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   3
  7Q LOSS WILD-TYPE  18 416
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE   18  416
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               3               416
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED     9   5
  8P LOSS WILD-TYPE 367  89
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               14               456 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5                89 
$`8P LOSS MUTATED`
TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-A66B TCGA-DU-7006 TCGA-DU-8165 TCGA-DU-A7TJ 
       50.86        19.96        42.05        11.47        19.13         0.56 
TCGA-E1-5304 TCGA-E1-A7YV TCGA-HT-7688 TCGA-HT-8564 TCGA-HT-A4DS TCGA-P5-A5F6 
       41.13        32.45        31.69        15.72         0.23         1.28 
TCGA-QH-A6CV TCGA-S9-A6WM 
       14.53        19.86 

$`8P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 
       12.10        11.24        17.88        30.74        16.18        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        30.21        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 
       16.83        94.52       114.08         7.96         7.73        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
       42.31        23.51         7.50        44.42        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       75.02        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       21.40        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.83        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.23              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            50.86            211.17 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           19.495            18.610 
[1] "0.2 - 50.9 (19.5)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "2.7"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     6   9
  8P LOSS WILD-TYPE 200 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      6    9
  8P LOSS WILD-TYPE  200  257
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               6               200
  MALE                 9               257
[1] 2 2
[1] FALSE
D55V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8P LOSS MUTATED             9                3                 3
  8P LOSS WILD-TYPE         167              115               175
D55V5, multiclass
                   clus
vv                  8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASTROCYTOMA                     9               167
  OLIGOASTROCYTOMA                3               115
  OLIGODENDROGLIOMA               3               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4  11
  8P LOSS WILD-TYPE  88 369
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4   11
  8P LOSS WILD-TYPE   88  369
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4                88
  YES              11               369
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     1
  8P LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           1    13
  8P LOSS WILD-TYPE                        14   424
D55V7, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         13               424
[1] 4 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, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1  14
  8P LOSS WILD-TYPE  17 405
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   14
  8P LOSS WILD-TYPE   17  405
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              14               405
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     6   3
  8Q LOSS WILD-TYPE 370  91
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               461 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                91 
$`8Q LOSS MUTATED`
TCGA-DH-5140 TCGA-DU-7006 TCGA-DU-8165 TCGA-E1-5304 TCGA-HT-8564 TCGA-HT-A4DS 
       19.96        11.47        19.13        41.13        15.72         0.23 
TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-S9-A6WM 
        1.28        14.53        19.86 

$`8Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.73        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV 
       13.78         0.23        29.59        34.19        28.27        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U 
        2.30         4.11         5.88         7.63         0.76         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        31.10        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.23              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            41.13            211.17 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            15.72             18.71 
[1] "0.2 - 41.1 (15.7)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "3.6"
D56V2, continuous
D56V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     5   4
  8Q LOSS WILD-TYPE 201 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    4
  8Q LOSS WILD-TYPE  201  262
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               5               201
  MALE                 4               262
[1] 2 2
[1] FALSE
D56V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8Q LOSS MUTATED             5                2                 2
  8Q LOSS WILD-TYPE         171              116               176
D56V5, multiclass
                   clus
vv                  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASTROCYTOMA                     5               171
  OLIGOASTROCYTOMA                2               116
  OLIGODENDROGLIOMA               2               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2   7
  8Q LOSS WILD-TYPE  90 373
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    7
  8Q LOSS WILD-TYPE   90  373
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                2                90
  YES               7               373
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     1
  8Q LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           0     8
  8Q LOSS WILD-TYPE                        15   429
D56V7, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          8               429
[1] 4 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, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1   8
  8Q LOSS WILD-TYPE  17 411
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    8
  8Q LOSS WILD-TYPE   17  411
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO               8               411
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    71  32
  9P LOSS WILD-TYPE 305  62
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              103               367 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               32                62 
$`9P LOSS MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6666 
       18.15        40.18        21.01         6.38        23.84         8.48 
TCGA-CS-6670 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC 
        6.61        50.86        44.52        78.28        30.21        46.72 
TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64V TCGA-DB-A75L TCGA-DB-A75P 
       33.57        31.63        24.20        29.23        11.24        16.18 
TCGA-DH-A7UR TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5855 TCGA-DU-6395 TCGA-DU-6397 
       54.25        18.02        17.46         6.81        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       65.75         7.04        11.64         7.73        11.47        62.96 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7301 
      117.40        90.77        26.30         7.96        18.94        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8162 TCGA-DU-8168 TCGA-DU-A5TY TCGA-DU-A6S7 
       23.31        41.98        14.60        14.17        12.20         7.23 
TCGA-DU-A6S8 TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 
        5.98        17.98        77.88         7.50         0.56        41.13 
TCGA-E1-5307 TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6690 
       57.93        14.33         0.20        25.48        36.82        24.99 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A711 
       18.44        17.88        14.24        18.38        18.71        48.69 
TCGA-FG-A87Q TCGA-HT-7471 TCGA-HT-7477 TCGA-HT-7606 TCGA-HT-7687 TCGA-HT-7689 
        5.72         0.13        24.26        17.29         0.10        14.96 
TCGA-HT-7692 TCGA-HT-7902 TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-A5RA TCGA-HT-A5RB 
        2.96        31.43        12.23         2.50        27.35         0.10 
TCGA-HT-A614 TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KM TCGA-IK-7675 
        2.70        19.23        21.60        17.82        20.71        19.00 
TCGA-P5-A5EV TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72Z TCGA-QH-A6CV 
        0.23         7.63         0.76         1.28        11.64        14.53 
TCGA-QH-A6CZ TCGA-RY-A83Z TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A7IS TCGA-S9-A7IX 
        9.17         9.90        62.17        37.84         7.92        22.32 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF 
        7.13        20.02       169.84        99.06        31.59        48.39 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8CB TCGA-VM-A8CD 
       30.44        24.16        15.98        26.99         0.10         7.89 
TCGA-W9-A837 
       51.06 

$`9P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 
        9.96        17.69        17.95        12.43         7.56         8.02 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        7.40       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE 
       50.17        36.56        46.42        18.84        39.78        37.45 
TCGA-DB-A4XG TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O 
       27.81        14.40        18.51        12.10        17.88        30.74 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT 
       42.05        27.81        17.19        17.19        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
        3.45        18.61        14.56         6.74        13.38         8.45 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6404 TCGA-DU-6405 
       22.42        75.16         1.22        87.45       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 
       16.83        94.52       114.08         7.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7290 
       14.99       105.21         6.54         8.84        30.67        10.36 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8158 
       94.32        44.02        62.01        60.30         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       23.74        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
        8.65         2.70        77.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5302 
       21.30       124.50        42.31        23.51        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       67.46        79.99       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O3 TCGA-FG-5962 
       75.02        32.45        36.82        32.35         0.23        47.77 
TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7638 
       34.36        18.77        14.93        23.97        15.35        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 
       20.61        20.09        12.95        13.68        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MY 
       14.96        22.52        32.61        38.27        10.72        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 
       28.54        10.78        36.66        20.45        13.58        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67        11.54        40.11         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18       122.47         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7690 
        0.76        44.68         6.05        42.74        31.69         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       37.87        33.01         6.25         0.10         0.46         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RC 
        0.23        26.04         0.13        20.22         0.07         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       29.92        19.89         8.32        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-8125 
       21.70        19.59        20.35        12.76        20.81        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40        14.40         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 
        4.11         5.88         0.16        10.42        13.25         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        19.33        14.83        13.61        12.23         2.20 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       59.38        30.87         5.46        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       30.67        87.12        18.77        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 
       15.16        14.07        36.13        23.51         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 
       17.03        15.06        13.12        28.37        13.02        10.39 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        24.92        16.18        59.05        40.64 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       28.08        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE 
       14.93        23.80        43.04        30.08        13.51        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-WH-A86K 
       23.47        37.05        16.01        23.21         8.05        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.10              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           169.84            211.17 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            18.44             18.71 
[1] "0.1 - 169.8 (18.4)" "0.0 - 211.2 (18.7)"
[1] "hr=" "2.1"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    44  60
  9P LOSS WILD-TYPE 162 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     44   60
  9P LOSS WILD-TYPE  162  206
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              44               162
  MALE                60               206
[1] 2 2
[1] FALSE
D57V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9P LOSS MUTATED            47               22                35
  9P LOSS WILD-TYPE         129               96               143
D57V5, multiclass
                   clus
vv                  9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASTROCYTOMA                    47               129
  OLIGOASTROCYTOMA               22                96
  OLIGODENDROGLIOMA              35               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"
D57V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    28  76
  9P LOSS WILD-TYPE  64 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     28   76
  9P LOSS WILD-TYPE   64  304
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               28                64
  YES              76               304
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     2
  9P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           3    95
  9P LOSS WILD-TYPE                        12   342
D57V7, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 6
  BLACK OR AFRICAN AMERICAN                      3                12
  WHITE                                         95               342
[1] 4 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, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     4  92
  9P LOSS WILD-TYPE  14 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4   92
  9P LOSS WILD-TYPE   14  327
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                14
  NOT HISPANIC OR LATINO              92               327
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    30  14
  9Q LOSS WILD-TYPE 346  80
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               44               426 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               14                80 
$`9Q LOSS MUTATED`
TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XH 
        6.38        23.84         8.48        50.86        44.52        31.63 
TCGA-DB-A64L TCGA-DB-A75P TCGA-DU-6397 TCGA-DU-7007 TCGA-DU-7014 TCGA-DU-7304 
       24.20        16.18        46.06        62.96       117.40        23.31 
TCGA-DU-8162 TCGA-DU-8168 TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A7T6 
       14.60        14.17        12.20         7.23         5.98        17.98 
TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5307 TCGA-EZ-7264 
       77.88         7.50         0.56        41.13        57.93        14.33 
TCGA-F6-A8O4 TCGA-FG-A87Q TCGA-HT-7471 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7692 
        0.20         5.72         0.13         0.10        14.96         2.96 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-P5-A72Z TCGA-P5-A733 
        0.10         2.70        19.00         1.28        11.64        13.61 
TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-S9-A6U9 TCGA-S9-A7IS TCGA-S9-A7R1 TCGA-TM-A84H 
       14.53         9.17        95.93         7.92       169.84        30.44 
TCGA-TM-A84J TCGA-TM-A84T 
       24.16        23.80 

$`9Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6290 
       40.18         0.10        21.01         9.96        17.69        17.95 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       12.43         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 
       81.96        75.25        47.93        72.92        50.17        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       78.28        46.42        18.84        30.21        46.72        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       37.45        33.57        72.95        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5141 
       12.10        11.24        17.88        30.74        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
      211.17        52.11        22.42        49.02        75.16        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 
       18.94        44.02        62.01        25.91        60.30        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        2.76         5.10        23.74        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       16.96        15.48        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K 
        3.65         5.65         8.65         2.70        77.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC 
       26.76         7.13        21.30       124.50        42.31        23.51 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
       44.42        50.14        67.46        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 
       36.66        48.69        20.45        13.58        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67        11.54        40.11         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 
       16.24         0.76        44.68         6.05        42.74        31.69 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 
        0.13        20.22         0.07        27.35         5.33        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.81        20.71        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 
        7.63         0.76         0.16        10.42        13.25         0.20 
TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        9.01        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 
       19.33        14.83        13.61        12.23         2.20        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       16.08        98.24         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY 
       18.61        15.16        14.07        36.13        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       13.12        28.37        13.02        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       40.64        28.08        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       18.61        14.93        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.10              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           169.84            211.17 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           14.565            18.805 
[1] "0.1 - 169.8 (14.6)" "0.0 - 211.2 (18.8)"
[1] "hr=" "1.8"
D58V2, continuous
D58V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    19  25
  9Q LOSS WILD-TYPE 187 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     19   25
  9Q LOSS WILD-TYPE  187  241
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              19               187
  MALE                25               241
[1] 2 2
[1] FALSE
D58V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9Q LOSS MUTATED            17               10                17
  9Q LOSS WILD-TYPE         159              108               161
D58V5, multiclass
                   clus
vv                  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASTROCYTOMA                    17               159
  OLIGOASTROCYTOMA               10               108
  OLIGODENDROGLIOMA              17               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     8  36
  9Q LOSS WILD-TYPE  84 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   36
  9Q LOSS WILD-TYPE   84  344
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                8                84
  YES              36               344
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     2
  9Q LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           1    39
  9Q LOSS WILD-TYPE                        14   398
D58V7, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 6
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         39               398
[1] 4 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, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2  40
  9Q LOSS WILD-TYPE  16 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   40
  9Q LOSS WILD-TYPE   16  379
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                16
  NOT HISPANIC OR LATINO              40               379
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    37  37
  10P LOSS WILD-TYPE 339  57
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                74                396 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                37                 57 
$`10P LOSS MUTATED`
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-DB-5279 
        7.69        21.01         6.38        17.69        23.84        44.52 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DH-5140 TCGA-DH-A669 TCGA-DU-5847 TCGA-DU-5852 
       24.20        25.48        19.96        30.21        18.02         6.74 
TCGA-DU-5854 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 
        8.45         7.04        11.64        19.89        16.83        11.47 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-8158 
        6.54         8.84        10.36         7.96        18.94         5.10 
TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L 
       23.74        19.13        15.48        12.20        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5311 TCGA-FG-6688 TCGA-FG-6692 
       21.30         7.50         0.56       134.27        18.77        18.44 
TCGA-FG-7643 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7471 
       20.09        10.72        18.38        10.78         5.72         0.13 
TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 
        0.23         0.49         3.72        16.24        12.23        13.78 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C 
       15.72         0.23        27.35         5.33        16.14        17.65 
TCGA-HT-A74H TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A72U TCGA-QH-A6CS TCGA-QH-A6CV 
        2.43        12.76        14.40         0.16        19.33        14.53 
TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A7IX 
        5.03        62.17        22.95         5.85        19.86        22.32 
TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J 
       10.39        18.71        49.45        24.92        28.08        24.16 
TCGA-VM-A8CD TCGA-VW-A8FI 
        7.89         8.05 

$`10P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 
        0.10         9.96        17.95        12.43         8.48         7.56 
TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 
        8.02         7.40         6.61       122.73        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        50.86        50.17        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       33.57        72.95        31.63        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       14.40         8.02        42.05        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 
       54.25        13.12        13.38         3.45        18.61        14.56 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       17.46        13.38         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6404 TCGA-DU-6407 
       46.06        65.75         1.22        87.45       133.74        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
      114.08         7.96         7.73        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99       105.21       117.40        90.77        30.67        26.30 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
       41.98         2.76        14.60        20.68        21.40        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
        5.65         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
        7.13        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       44.42        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
       34.36        36.82        14.93        24.99        23.97        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       17.88        22.55        20.61        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        22.26        28.54        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       13.58        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       19.23        39.09        50.63        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 
        0.13         3.68         5.33        35.47        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
        1.64         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 
        6.25         0.10         0.46         2.50         5.56         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       29.59        34.19        28.27        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 
        0.07         0.10         2.70        16.93         1.81        16.83 
TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       21.40        17.52        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV 
       20.81        20.71        19.00        42.77        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        7.63         0.76         1.28        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       15.85        14.04        14.83        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.50        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       19.59        30.67        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       31.33        28.70        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        31.10        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.07        36.13         7.92        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02       169.84        99.06        30.05        98.63        31.59 
TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C 
       11.97        48.33        49.32        34.78        48.39        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       59.05        40.64        30.44        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       43.04        30.08        13.51         0.10        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       37.05        16.01        23.21        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.13               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            134.27             211.17 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            15.005             19.955 
[1] "0.1 - 134.3 (15.0)" "0.0 - 211.2 (20.0)"
[1] "hr=" "8.1"
D59V2, continuous
D59V3, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    34  40
  10P LOSS WILD-TYPE 172 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     34   40
  10P LOSS WILD-TYPE  172  226
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               34                172
  MALE                 40                226
[1] 2 2
[1] FALSE
D59V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10P LOSS MUTATED            44               14                16
  10P LOSS WILD-TYPE         132              104               162
D59V5, multiclass
                   clus
vv                  10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASTROCYTOMA                     44                132
  OLIGOASTROCYTOMA                14                104
  OLIGODENDROGLIOMA               16                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    12  62
  10P LOSS WILD-TYPE  80 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     12   62
  10P LOSS WILD-TYPE   80  318
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                12                 80
  YES               62                318
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  1     1
  10P LOSS WILD-TYPE                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           6    65
  10P LOSS WILD-TYPE                         9   372
D59V7, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       6                  9
  WHITE                                          65                372
[1] 4 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, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  67
  10P LOSS WILD-TYPE  16 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   67
  10P LOSS WILD-TYPE   16  352
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               67                352
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    44  43
  10Q LOSS WILD-TYPE 332  51
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                87                383 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                43                 51 
$`10Q LOSS MUTATED`
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 
        7.69        21.01         6.38        17.69        23.84        12.43 
TCGA-DB-5279 TCGA-DB-A64L TCGA-DB-A64O TCGA-DH-5140 TCGA-DH-A669 TCGA-DH-A7UU 
       44.52        24.20        25.48        19.96        30.21         3.45 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6402 
       18.02         6.74         8.45        75.16        65.75         7.04 
TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 
       11.64        19.89        16.83        11.47       156.23        14.99 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 
        6.54         8.84       117.40        10.36         7.96        18.94 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TY TCGA-DU-A76K 
        5.10        23.74        19.13        15.48        12.20        11.41 
TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5311 TCGA-E1-A7YV 
       26.76        21.30         7.50         0.56       134.27        32.45 
TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 
       18.77        18.44        20.09        10.72        18.38        22.26 
TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7471 TCGA-HT-7483 TCGA-HT-7857 TCGA-HT-7860 
       10.78         5.72         0.13       172.77         0.23         0.49 
TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS 
        3.72        16.24        12.23        13.78        15.72         0.23 
TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H 
       20.22        27.35         5.33        16.14        17.65         2.43 
TCGA-HW-8321 TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EZ TCGA-P5-A72U TCGA-QH-A6CS 
       19.59        12.76        14.40         2.30         0.16        19.33 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6U0 TCGA-S9-A6UA 
       14.53        12.23         5.03        62.17        22.95         5.85 
TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84I 
       19.86        22.32        10.39        49.45        24.92        28.08 
TCGA-TM-A84J TCGA-VM-A8CD TCGA-VW-A8FI 
       24.16         7.89         8.05 

$`10Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
        0.10         9.96        17.95         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.86        50.17        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        31.63        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       17.88        30.74        16.18        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
        8.02        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
       13.12        13.38        18.61        14.56        17.46        13.38 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 
       52.11        22.42        49.02        46.06         1.22        87.45 
TCGA-DU-6404 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 
      133.74        94.52       114.08         7.96         7.73        62.96 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 
      138.28       105.21        90.77        30.67        26.30        94.32 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 
        2.76        14.60        20.68        21.40        16.96        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O 
        8.65         2.70        77.98         7.23         5.98         7.13 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG 
       17.98       124.50        77.88        42.31        23.51        44.42 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 
       50.14        67.46        41.13        79.99        57.93        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
       95.57       130.78        75.02        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       14.93        24.99        23.97        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.61        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       14.96        22.52        32.61        38.27        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y 
       14.76        17.82        16.41        15.02        16.44        28.54 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 
       36.66        48.69        20.45        13.58        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67        11.54        40.11         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       95.93       106.95         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7873 
       14.53        39.48        19.23        39.09        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28        31.43         1.64         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV 
        5.56         0.23        29.59        34.19        28.27        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
        0.13         0.07         0.10         2.70        16.93         1.81 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       16.83        21.40        17.52        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.90         4.31        21.70        21.60        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV 
       20.81        20.71        19.00        42.77        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        6.71         1.64         2.37         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        0.76         1.28        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.04        14.83        13.61         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A86X 
       14.53        16.34        16.73         1.91        16.50        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       48.33        49.32        34.78        48.39        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       40.64        30.44        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08        13.51         0.10        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.13               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            172.77             211.17 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             15.72              19.59 
[1] "0.1 - 172.8 (15.7)" "0.0 - 211.2 (19.6)"
[1] "hr=" "5.2"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    41  46
  10Q LOSS WILD-TYPE 165 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     41   46
  10Q LOSS WILD-TYPE  165  220
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               41                165
  MALE                 46                220
[1] 2 2
[1] FALSE
D60V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10Q LOSS MUTATED            51               17                19
  10Q LOSS WILD-TYPE         125              101               159
D60V5, multiclass
                   clus
vv                  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASTROCYTOMA                     51                125
  OLIGOASTROCYTOMA                17                101
  OLIGODENDROGLIOMA               19                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    15  72
  10Q LOSS WILD-TYPE  77 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     15   72
  10Q LOSS WILD-TYPE   77  308
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                15                 77
  YES               72                308
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  1     1
  10Q LOSS WILD-TYPE                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           6    78
  10Q LOSS WILD-TYPE                         9   359
D60V7, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       6                  9
  WHITE                                          78                359
[1] 4 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, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     2  80
  10Q LOSS WILD-TYPE  16 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   80
  10Q LOSS WILD-TYPE   16  339
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               80                339
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    40  17
  11P LOSS WILD-TYPE 336  77
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                57                413 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                17                 77 
$`11P LOSS MUTATED`
TCGA-CS-6665 TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A66G TCGA-DH-A7UT 
       12.43        50.86        19.96        30.31        17.19        13.38 
TCGA-DH-A7UU TCGA-DU-6396 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
        3.45        75.16       114.08        11.47        62.96       156.23 
TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-A5TR 
       14.99       117.40        90.77         5.10        19.13        12.59 
TCGA-DU-A5TS TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-A7YV TCGA-FG-6689 TCGA-FG-A4MW 
       15.12        50.14        41.13        32.45        14.93        18.38 
TCGA-FG-A60L TCGA-HT-7470 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7601 TCGA-HT-7686 
       16.41        40.11        24.26         6.38         5.03        42.74 
TCGA-HT-7693 TCGA-HT-7873 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8111 
       17.52        23.61        31.43        63.55        37.87         0.23 
TCGA-HT-8564 TCGA-HT-A5R7 TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B 
       15.72        20.22         2.70         1.81        16.83        17.52 
TCGA-HW-8319 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-RY-A83Z TCGA-S9-A6TV 
       21.70        19.00         1.28         2.53         9.90        18.77 
TCGA-S9-A6WM TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       19.86        98.63        18.71        11.97        49.45        48.33 
TCGA-TM-A84I TCGA-TM-A84J TCGA-WY-A859 
       28.08        24.16        39.88 

$`11P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 
       11.24        17.88        30.74        16.18        31.82        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR 
        8.02        30.21        42.05        27.81        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.12        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 
       15.16       211.17        52.11        22.42        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7009 
       19.89        16.83        94.52         7.96         7.73       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
      105.21         6.54         8.84        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31        41.98         2.76        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
        7.50        44.42         0.56        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW 
      134.27        78.21        95.57       130.78        75.02        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       34.36        36.82        18.77        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       32.61        38.27        10.72        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67        11.54         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        3.75        17.42         6.54        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      106.95       172.77         4.01        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
       44.68         6.05         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10         2.96         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23        50.63         0.49        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 
        1.64        16.24         9.40         0.10        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        28.27         0.23        26.04         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A617 
        0.07        27.35         0.10         5.33        16.93        16.14 
TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       21.40        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.90         4.31        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        20.81        20.71        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        5.88         7.63         0.76         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65V 
       11.64         0.20         9.01        13.61        15.16        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C5 
      169.84        10.39        99.06        30.05        31.59        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       30.44        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.23               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            156.23             211.17 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             19.13              18.51 
[1] "0.2 - 156.2 (19.1)" "0.0 - 211.2 (18.5)"
[1] "hr=" "1.4"
D61V2, continuous
D61V3, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    29  28
  11P LOSS WILD-TYPE 177 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     29   28
  11P LOSS WILD-TYPE  177  238
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               29                177
  MALE                 28                238
[1] 2 2
[1] FALSE
D61V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11P LOSS MUTATED            32               13                12
  11P LOSS WILD-TYPE         144              105               166
D61V5, multiclass
                   clus
vv                  11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASTROCYTOMA                     32                144
  OLIGOASTROCYTOMA                13                105
  OLIGODENDROGLIOMA               12                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    14  43
  11P LOSS WILD-TYPE  78 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     14   43
  11P LOSS WILD-TYPE   78  337
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                14                 78
  YES               43                337
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           1    56
  11P LOSS WILD-TYPE                        14   381
D61V7, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          56                381
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  54
  11P LOSS WILD-TYPE  16 365
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   54
  11P LOSS WILD-TYPE   16  365
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               54                365
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    13   7
  11Q LOSS WILD-TYPE 363  87
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                20                450 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 87 
$`11Q LOSS MUTATED`
TCGA-DH-5140 TCGA-DU-7006 TCGA-DU-7010 TCGA-DU-8158 TCGA-DU-8165 TCGA-E1-5304 
       19.96        11.47        14.99         5.10        19.13        41.13 
TCGA-FG-A4MW TCGA-HT-7477 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A5R7 
       18.38        24.26        37.87         0.23        15.72        20.22 
TCGA-HT-A614 TCGA-HT-A61B TCGA-P5-A5F6 TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A89V 
        2.70        17.52         1.28        18.77        19.86        18.71 
TCGA-TM-A7C3 TCGA-TM-A84I 
       49.45        28.08 

$`11Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
        7.73        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31        41.98         2.76        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       38.27        10.72        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS 
        5.56        13.78        29.59        34.19        28.27         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04         0.13         0.07        27.35         0.10         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C 
       16.93         1.81        16.14        16.83        21.40        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        5.88         7.63         0.76         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       62.17        87.12        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        31.10        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       98.63        31.59        11.97        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.23               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             49.45             211.17 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             18.74              18.61 
[1] "0.2 - 49.5 (18.7)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "3.2"
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     9  11
  11Q LOSS WILD-TYPE 197 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      9   11
  11Q LOSS WILD-TYPE  197  255
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                9                197
  MALE                 11                255
[1] 2 2
[1] FALSE
D62V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11Q LOSS MUTATED            12                6                 2
  11Q LOSS WILD-TYPE         164              112               176
D62V5, multiclass
                   clus
vv                  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASTROCYTOMA                     12                164
  OLIGOASTROCYTOMA                 6                112
  OLIGODENDROGLIOMA                2                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2  18
  11Q LOSS WILD-TYPE  90 362
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   18
  11Q LOSS WILD-TYPE   90  362
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 2                 90
  YES               18                362
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     0
  11Q LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           0    20
  11Q LOSS WILD-TYPE                        15   417
D62V7, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          20                417
[1] 4 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, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  19
  11Q LOSS WILD-TYPE  17 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   19
  11Q LOSS WILD-TYPE   17  400
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               19                400
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    19   4
  12P LOSS WILD-TYPE 357  90
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                23                447 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 90 
$`12P LOSS MUTATED`
TCGA-CS-6665 TCGA-DB-5279 TCGA-DB-A4XH TCGA-DU-5871 TCGA-DU-6542 TCGA-DU-A6S6 
       12.43        44.52        31.63        18.94         7.73        77.98 
TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-A7YV TCGA-FG-A6J3 TCGA-HT-7470 TCGA-HT-7478 
       21.30        50.14        32.45        22.26        40.11         6.38 
TCGA-HT-7686 TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-A5R7 TCGA-HT-A61B TCGA-P5-A5EW 
       42.74         0.10         2.50        20.22        17.52         6.71 
TCGA-P5-A5F4 TCGA-P5-A72X TCGA-S9-A6U1 TCGA-S9-A7R4 TCGA-S9-A89V 
        0.76        13.25        17.62        30.05        18.71 

$`12P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.86        50.17        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
       94.52       114.08         7.96        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
        7.13        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        7.50        44.42         0.56        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       24.26        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         6.25         0.46 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
       15.72         0.23        26.04         0.13         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.83        21.40        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY 
       42.77        14.40        14.40         0.23         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U 
        2.30         4.11         5.88         7.63         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       10.42        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       31.33        28.70        22.95        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       99.06        98.63        31.59        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.10               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             77.98             211.17 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             18.94              18.61 
[1] "0.1 - 78.0 (18.9)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.2"
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    12  12
  12P LOSS WILD-TYPE 194 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12   12
  12P LOSS WILD-TYPE  194  254
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               12                194
  MALE                 12                254
[1] 2 2
[1] FALSE
D63V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12P LOSS MUTATED            14                5                 5
  12P LOSS WILD-TYPE         162              113               173
D63V5, multiclass
                   clus
vv                  12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASTROCYTOMA                     14                162
  OLIGOASTROCYTOMA                 5                113
  OLIGODENDROGLIOMA                5                173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     5  19
  12P LOSS WILD-TYPE  87 361
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5   19
  12P LOSS WILD-TYPE   87  361
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 5                 87
  YES               19                361
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     0
  12P LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           0    23
  12P LOSS WILD-TYPE                        15   414
D63V7, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          23                414
[1] 4 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, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  23
  12P LOSS WILD-TYPE  18 396
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   23
  12P LOSS WILD-TYPE   18  396
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               23                396
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    38   7
  12Q LOSS WILD-TYPE 338  87
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                45                425 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 7                 87 
$`12Q LOSS MUTATED`
TCGA-CS-6665 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XH TCGA-DH-A66B 
       12.43        47.93        50.86        44.52        31.63        42.05 
TCGA-DU-5871 TCGA-DU-6401 TCGA-DU-6542 TCGA-DU-8167 TCGA-DU-A5TU TCGA-DU-A6S6 
       18.94        87.45         7.73        15.48         3.65        77.98 
TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-A7YV TCGA-FG-6689 TCGA-HT-7470 TCGA-HT-7474 
       21.30        50.14        32.45        14.93        40.11         3.75 
TCGA-HT-7478 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7902 TCGA-HT-8018 
        6.38        42.74        31.69         0.10        31.43        37.87 
TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-A5R7 TCGA-HT-A618 TCGA-HT-A61B TCGA-P5-A5EW 
        0.10         2.50        20.22        16.83        17.52         6.71 
TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A72X TCGA-S9-A6TV TCGA-S9-A6U1 
        2.30         0.76        10.42        13.25        18.77        17.62 
TCGA-S9-A6WQ TCGA-S9-A7QX TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-TM-A84I 
       14.07        13.12        30.05        98.63        18.71        28.08 
TCGA-VM-A8C8 TCGA-WH-A86K TCGA-WY-A85B 
       43.04        13.32        45.80 

$`12Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 
        6.61       122.73        81.96        75.25        72.92        50.17 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O 
       39.78        37.45        33.57        72.95        24.20        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       14.40        18.51        12.10        11.24        17.88        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       16.18        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75         1.22         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.96        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 
       14.60        20.68        21.40        19.13        16.96        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59        15.12         4.96         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
        7.13        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        7.50        44.42         0.56        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 
       25.48        34.36        36.82        18.77        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.13         0.03        16.54        17.42         6.54        24.26 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
        0.10        14.96         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47         3.72        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55         0.10        33.01        12.23         6.25 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.46         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       28.27        15.72         0.23        26.04         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.14        21.40        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY 
       42.77        14.40        14.40         0.23         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72Z 
        4.11         5.88         7.63         1.28         0.16        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       87.12        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7IQ 
       31.10        19.86        15.91        18.61        15.16        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        17.03        15.06        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       10.39        99.06        31.59        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       40.64        30.44        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 
       37.05        16.01        23.21         8.05        51.06        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        46.88        37.71        20.81 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.10               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             98.63             211.17 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             18.77              18.61 
[1] "0.1 - 98.6 (18.8)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.2"
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    20  26
  12Q LOSS WILD-TYPE 186 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     20   26
  12Q LOSS WILD-TYPE  186  240
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               20                186
  MALE                 26                240
[1] 2 2
[1] FALSE
D64V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12Q LOSS MUTATED            25               13                 8
  12Q LOSS WILD-TYPE         151              105               170
D64V5, multiclass
                   clus
vv                  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASTROCYTOMA                     25                151
  OLIGOASTROCYTOMA                13                105
  OLIGODENDROGLIOMA                8                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    10  36
  12Q LOSS WILD-TYPE  82 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     10   36
  12Q LOSS WILD-TYPE   82  344
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                10                 82
  YES               36                344
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           0    45
  12Q LOSS WILD-TYPE                        15   392
D64V7, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          45                392
[1] 4 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, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  43
  12Q LOSS WILD-TYPE  18 376
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   43
  12Q LOSS WILD-TYPE   18  376
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               43                376
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    80  25
  13Q LOSS WILD-TYPE 296  69
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               105                365 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                25                 69 
$`13Q LOSS MUTATED`
TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6670 TCGA-DB-5275 TCGA-DB-5277 
       18.15        17.95         8.48         6.61        47.93        50.86 
TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 
       18.84        37.45        18.51        19.96        30.31        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5853 TCGA-DU-6392 
       27.81        17.19         3.45        18.02        13.38       211.17 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7008 
       65.75         1.22        94.52       114.08        11.47       156.23 
TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-8158 TCGA-DU-8165 
       14.99        10.36        44.02        25.91         5.10        19.13 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A76R 
       15.48        14.17        15.12         2.70         7.23        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 
      124.50        77.88        50.14        67.46        41.13        57.93 
TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-6692 
      130.78        47.77        25.48        34.36        14.93        18.44 
TCGA-FG-7641 TCGA-FG-8188 TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J3 
       20.61        14.96        14.76        16.41        15.02        22.26 
TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7476 
       10.78         5.72        11.54        40.11         0.13         6.54 
TCGA-HT-7477 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
       24.26       106.95       172.77       122.47         4.57        17.29 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-7857 
       31.69        14.96         0.10         2.96        39.09         0.23 
TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8564 TCGA-HT-A617 TCGA-HT-A61B TCGA-HW-7489 
       31.43         0.10        15.72        16.14        17.52         8.32 
TCGA-HW-7491 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A72W TCGA-QH-A65Z 
       40.18        14.40         2.30         0.76        10.42        14.04 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X8 TCGA-RY-A83Z TCGA-RY-A847 
       14.53        13.61         2.20        16.73         9.90        30.67 
TCGA-S9-A6UA TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A89V 
        5.85        22.32        23.51        20.02        17.03        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84R TCGA-TM-A84S 
       11.97        49.45        59.05        28.08        18.61        14.93 
TCGA-TQ-A7RH TCGA-VM-A8CD TCGA-WY-A85E 
       15.98         7.89        20.81 

$`13Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       12.43         7.56         8.02         7.40       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       75.25        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       46.42        30.21        46.72        39.78        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L 
       27.45        27.81        29.23        14.40        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 
       17.88        30.74        16.18        31.82        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV 
       42.05        17.19        54.25        13.12        13.38        18.61 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       14.56        17.46         6.74         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       75.16        46.06        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 
       19.89        16.83         7.96         7.73        62.96       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 
       26.30         7.96        94.32        18.94        62.01        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         2.76        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       21.40        16.96        14.24        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
        5.65        12.20         8.65        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       26.76         7.13        17.98        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       44.42         0.56        79.99       134.27        78.21        95.57 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
        0.20        36.82        18.77        24.99        23.97        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       17.88        22.55        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        20.09        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A6J1 TCGA-FG-A70Y 
       18.38        18.71        23.70        17.82        16.44        28.54 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 
       36.66        48.69        20.45        13.58        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 
        6.67         0.03        16.54         3.75        17.42         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       40.34        75.19        95.93         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       23.18         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 
        6.05        42.74         0.10         0.10        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       14.53        39.48        19.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        3.72        11.28         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         6.25         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       28.27         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.83        21.40        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7493 
       11.05         0.10        29.92        19.89        19.23        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A7W1 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        7.63         1.28         0.16        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       19.33        14.83        12.23         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       28.08         2.07        19.59        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       23.64        32.61        16.08        98.24        95.93       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7QX 
        7.92         7.13         8.19         2.04        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       98.63        31.59        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L 
       24.92        16.18        40.64        30.44        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RW TCGA-VM-A8C8 
       24.79        33.24        25.38        23.80        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08        13.51         0.10        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       39.88        43.40        45.80        46.88        37.71 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.10               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            211.17             182.33 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             17.95              19.00 
[1] "0.1 - 211.2 (17.9)" "0.0 - 182.3 (19.0)"
[1] "hr=" "1.1"
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    38  67
  13Q LOSS WILD-TYPE 168 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     38   67
  13Q LOSS WILD-TYPE  168  199
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               38                168
  MALE                 67                199
[1] 2 2
[1] FALSE
D65V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  13Q LOSS MUTATED            44               24                37
  13Q LOSS WILD-TYPE         132               94               141
D65V5, multiclass
                   clus
vv                  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASTROCYTOMA                     44                132
  OLIGOASTROCYTOMA                24                 94
  OLIGODENDROGLIOMA               37                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"
D65V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    30  75
  13Q LOSS WILD-TYPE  62 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     30   75
  13Q LOSS WILD-TYPE   62  305
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                30                 62
  YES               75                305
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     1
  13Q LOSS WILD-TYPE                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           3    98
  13Q LOSS WILD-TYPE                        12   339
D65V7, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       3                 12
  WHITE                                          98                339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     3  96
  13Q LOSS WILD-TYPE  15 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3   96
  13Q LOSS WILD-TYPE   15  323
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 15
  NOT HISPANIC OR LATINO               96                323
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    45  24
  14Q LOSS WILD-TYPE 331  70
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                69                401 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                24                 70 
$`14Q LOSS MUTATED`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-6668 TCGA-DB-5279 TCGA-DB-A4XA 
        4.70         7.69        43.89         8.02        44.52        18.84 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DU-5847 
       24.20        25.48        19.96        30.31        14.40        18.02 
TCGA-DU-5852 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7010 
        6.74        46.06        65.75         7.73        62.96        14.99 
TCGA-DU-7012 TCGA-DU-7290 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 
        6.54        10.36        60.30         5.10        23.74        19.13 
TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76R TCGA-E1-5305 TCGA-E1-5322 TCGA-EZ-7264 
        5.98        26.76        21.30        79.99       130.78        14.33 
TCGA-FG-7643 TCGA-FG-8191 TCGA-FG-A6J3 TCGA-HT-7477 TCGA-HT-7616 TCGA-HT-7688 
       20.09        32.61        22.26        24.26         0.23        31.69 
TCGA-HT-7689 TCGA-HT-7902 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A617 
       14.96        31.43        13.78        15.72         0.23        16.14 
TCGA-HT-A618 TCGA-HT-A61C TCGA-HW-7489 TCGA-HW-A5KK TCGA-IK-8125 TCGA-P5-A5EX 
       16.83        17.65         8.32        12.76        42.77         1.64 
TCGA-P5-A5EZ TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CZ TCGA-RY-A83Z 
        2.30        19.33        14.53        13.61         9.17         9.90 
TCGA-RY-A840 TCGA-S9-A6TS TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7QZ TCGA-S9-A7R2 
       28.08        62.17        19.86        22.32        13.02        10.39 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84I TCGA-VM-A8CB TCGA-VM-A8CD 
       31.59        18.71        49.45        28.08         0.10         7.89 
TCGA-VV-A829 TCGA-WY-A858 TCGA-WY-A85B 
       37.05        43.96        45.80 

$`14Q LOSS WILD-TYPE`
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 
       18.15        10.62        64.64        40.18         0.10        21.01 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
        9.96         6.38        17.69        23.84        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
        8.48         7.56         7.40         6.61       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 
       75.25        47.93        72.92        50.86        50.17        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       78.28        46.42        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       33.57        72.95        31.63        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5144 
       11.24        17.88        30.74        16.18        31.82         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       30.21        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 
       13.12        13.38         3.45        18.61        14.56        17.46 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 
       16.83        94.52       114.08         7.96        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      138.28       105.21         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       26.30         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 
       25.91        23.31        41.98         2.76        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A7T6 
        2.70        77.98         7.23        11.41         7.13        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5311 
        0.56        50.14        67.46        41.13        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       78.21        95.57        75.02        32.45        36.82        32.35 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       17.88        22.55        20.61        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        20.09        14.96        22.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       56.09        57.60        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 
       44.68         6.05        42.74         0.10         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        2.50         5.56         0.23        29.59        34.19        28.27 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A619 TCGA-HT-A61B 
        5.33         2.70        16.93         1.81        21.40        17.52 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       19.89        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM 
       21.60        19.59        17.82        20.35        20.81        20.71 
TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY 
       19.00        14.40        14.40         0.23         6.71         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
       15.16         2.53        12.62        15.85        14.04        14.83 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       12.23         2.20        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A843 
       94.03        32.65        59.38        30.87         5.46         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       19.59        30.67        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        31.10        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY 
       18.61        15.16        14.07        36.13         7.92        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.12        28.37       169.84        99.06        30.05        98.63 
TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       11.97        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        40.64        30.44        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE 
       15.98        26.99        43.04        30.08        13.51        35.93 
TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       23.47        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        46.88        37.71        20.81 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.10               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            130.78             211.17 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             18.84              18.61 
[1] "0.1 - 130.8 (18.8)" "0.0 - 211.2 (18.6)"
[1] "hr=" "2.6"
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    30  40
  14Q LOSS WILD-TYPE 176 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     30   40
  14Q LOSS WILD-TYPE  176  226
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               30                176
  MALE                 40                226
[1] 2 2
[1] FALSE
D66V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  14Q LOSS MUTATED            33               16                21
  14Q LOSS WILD-TYPE         143              102               157
D66V5, multiclass
                   clus
vv                  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASTROCYTOMA                     33                143
  OLIGOASTROCYTOMA                16                102
  OLIGODENDROGLIOMA               21                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    11  59
  14Q LOSS WILD-TYPE  81 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11   59
  14Q LOSS WILD-TYPE   81  321
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                11                 81
  YES               59                321
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  1     1
  14Q LOSS WILD-TYPE                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           2    63
  14Q LOSS WILD-TYPE                        13   374
D66V7, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          63                374
[1] 4 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, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  60
  14Q LOSS WILD-TYPE  17 359
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   60
  14Q LOSS WILD-TYPE   17  359
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               60                359
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    33  12
  15Q LOSS WILD-TYPE 343  82
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                45                425 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                 82 
$`15Q LOSS MUTATED`
TCGA-DB-5274 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XH TCGA-DH-5140 TCGA-DH-5142 
       75.25        44.52        18.84        31.63        19.96        30.31 
TCGA-DH-A669 TCGA-DH-A7UT TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-7007 TCGA-DU-8158 
       30.21        13.38        52.11         1.22        62.96         5.10 
TCGA-DU-A6S3 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TC TCGA-E1-5311 TCGA-FG-7634 
        2.70        21.30        17.98        23.51       134.27        15.35 
TCGA-FG-7636 TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-HT-7468 TCGA-HT-7480 TCGA-HT-7606 
       17.88        18.38        22.26         6.67        75.19        17.29 
TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-8012 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       45.99         0.23         9.40        16.83        21.40        17.52 
TCGA-HT-A74K TCGA-P5-A5EZ TCGA-QH-A65S TCGA-QH-A6X8 TCGA-RY-A83X TCGA-S9-A6TS 
       15.35         2.30         2.53        16.73        30.87        62.17 
TCGA-S9-A6U2 TCGA-S9-A6WD TCGA-S9-A6WI TCGA-S9-A7QZ TCGA-S9-A89Z TCGA-TM-A7C5 
       23.64        69.50        84.99        13.02        11.97        49.32 
TCGA-VV-A86M TCGA-W9-A837 TCGA-WY-A85D 
       16.01        51.06        37.71 

$`15Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       50.86        50.17        36.56        78.28        46.42        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L 
       46.72        39.78        37.45        33.57        72.95        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       30.74        16.18        31.82        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU 
       27.81        17.19        17.19        54.25        13.12         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
      211.17        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         2.76        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
      124.50        77.88        42.31         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 
       50.14        67.46        41.13        79.99        57.93        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       10.72        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 
       20.45        13.58         5.72        27.52         0.10        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 
        6.54        24.26         6.38        40.34        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 
        4.57         3.16        22.06        56.09        57.60        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
       31.43         1.64        16.24        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74L TCGA-HT-A74O 
       16.14        17.65         2.43        10.52        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
       14.40         0.23         6.71         1.64         2.37         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        59.38         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV 
       28.08         2.07        19.59        30.67        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        32.45        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        13.12        28.37       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        31.59        18.71        49.45        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VW-A7QS TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 
       23.47        37.05        23.21         8.05        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        20.81 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.23               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            134.27             211.17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             19.96              18.61 
[1] "0.2 - 134.3 (20.0)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1.3"
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    19  27
  15Q LOSS WILD-TYPE 187 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19   27
  15Q LOSS WILD-TYPE  187  239
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               19                187
  MALE                 27                239
[1] 2 2
[1] FALSE
D67V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  15Q LOSS MUTATED            15               10                21
  15Q LOSS WILD-TYPE         161              108               157
D67V5, multiclass
                   clus
vv                  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASTROCYTOMA                     15                161
  OLIGOASTROCYTOMA                10                108
  OLIGODENDROGLIOMA               21                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     8  38
  15Q LOSS WILD-TYPE  84 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8   38
  15Q LOSS WILD-TYPE   84  342
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 8                 84
  YES               38                342
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     1
  15Q LOSS WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           0    43
  15Q LOSS WILD-TYPE                        15   394
D67V7, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          43                394
[1] 4 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, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  43
  15Q LOSS WILD-TYPE  17 376
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   43
  15Q LOSS WILD-TYPE   17  376
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               43                376
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     6   5
  16P LOSS WILD-TYPE 370  89
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                459 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 89 
$`16P LOSS MUTATED`
TCGA-DB-5277 TCGA-DB-5281 TCGA-DH-A669 TCGA-DU-7018 TCGA-DU-8165 TCGA-E1-5307 
       50.86        78.28        30.21        30.67        19.13        57.93 
TCGA-FG-A4MW TCGA-HT-7477 TCGA-HT-8564 TCGA-S9-A7IX TCGA-S9-A89V 
       18.38        24.26        15.72        22.32        18.71 

$`16P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA 
       72.92        50.17        44.52        36.56        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84       117.40        90.77        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        41.13        79.99       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       38.27        10.72        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       28.27         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.14        16.83        21.40        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY 
       18.61        15.16        14.07        36.13         7.92        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        31.59        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             15.72               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             78.28             211.17 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             24.26              18.51 
[1] "15.7 - 78.3 (24.3)" "0.0 - 211.2 (18.5)"
[1] "hr=" "2"  
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3   8
  16P LOSS WILD-TYPE 203 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    8
  16P LOSS WILD-TYPE  203  258
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                203
  MALE                  8                258
[1] 2 2
[1] FALSE
D68V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16P LOSS MUTATED             6                2                 3
  16P LOSS WILD-TYPE         170              116               175
D68V5, multiclass
                   clus
vv                  16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASTROCYTOMA                      6                170
  OLIGOASTROCYTOMA                 2                116
  OLIGODENDROGLIOMA                3                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     2   9
  16P LOSS WILD-TYPE  90 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    9
  16P LOSS WILD-TYPE   90  371
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 2                 90
  YES                9                371
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           0    11
  16P LOSS WILD-TYPE                        15   426
D68V7, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          11                426
[1] 4 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, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1  10
  16P LOSS WILD-TYPE  17 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   10
  16P LOSS WILD-TYPE   17  409
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               10                409
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    11   8
  16Q LOSS WILD-TYPE 365  86
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                19                451 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 8                 86 
$`16Q LOSS MUTATED`
TCGA-DB-5277 TCGA-DB-5281 TCGA-DH-A669 TCGA-DU-5847 TCGA-DU-7012 TCGA-DU-7014 
       50.86        78.28        30.21        18.02         6.54       117.40 
TCGA-DU-7018 TCGA-DU-8165 TCGA-DU-8167 TCGA-E1-5307 TCGA-FG-A4MW TCGA-HT-7469 
       30.67        19.13        15.48        57.93        18.38        11.54 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-S9-A6U9 TCGA-S9-A6WH TCGA-S9-A7IX TCGA-S9-A89V 
       15.72         0.23        95.93        32.45        22.32        18.71 
TCGA-S9-A89Z 
       11.97 

$`16Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA 
       72.92        50.17        44.52        36.56        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 
      156.23       138.28        14.99       105.21         8.84        90.77 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        5.10        23.74        14.60        20.68        21.40        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 
        0.56        50.14        67.46        41.13        79.99       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY 
       22.52        32.61        38.27        10.72        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 
        5.72        27.52         0.10         6.67        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       29.59        34.19        28.27        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       16.08        98.24         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       80.12        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ 
       15.16        14.07        36.13         7.92        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       98.63        31.59        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.23               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            117.40             211.17 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             19.13              18.61 
[1] "0.2 - 117.4 (19.1)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1.8"
D69V2, continuous
D69V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     8  11
  16Q LOSS WILD-TYPE 198 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8   11
  16Q LOSS WILD-TYPE  198  255
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                8                198
  MALE                 11                255
[1] 2 2
[1] FALSE
D69V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16Q LOSS MUTATED            10                4                 5
  16Q LOSS WILD-TYPE         166              114               173
D69V5, multiclass
                   clus
vv                  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASTROCYTOMA                     10                166
  OLIGOASTROCYTOMA                 4                114
  OLIGODENDROGLIOMA                5                173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5  14
  16Q LOSS WILD-TYPE  87 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   14
  16Q LOSS WILD-TYPE   87  366
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 5                 87
  YES               14                366
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           1    18
  16Q LOSS WILD-TYPE                        14   419
D69V7, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          18                419
[1] 4 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, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  18
  16Q LOSS WILD-TYPE  17 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   18
  16Q LOSS WILD-TYPE   17  401
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               18                401
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED     9   3
  17P LOSS WILD-TYPE 367  91
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                458 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 91 
$`17P LOSS MUTATED`
TCGA-DU-6400 TCGA-DU-7010 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TP TCGA-FG-A4MY 
        1.22        14.99        23.74        19.13        14.24        23.70 
TCGA-HT-7689 TCGA-HT-8106 TCGA-HT-8564 TCGA-HT-A4DS TCGA-P5-A5EZ TCGA-P5-A5F6 
       14.96         0.10        15.72         0.23         2.30         1.28 

$`17P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.73        11.47        62.96       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       14.60        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J 
       32.61        38.27        10.72        18.38        18.71        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        31.69         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         6.25         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
       28.27        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        1.64         2.37         4.11         5.88         7.63         0.76 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             23.74             211.17 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             14.60              18.77 
[1] "0.1 - 23.7 (14.6)"  "0.0 - 211.2 (18.8)"
[1] "hr=" "4.4"
D70V2, continuous
D70V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     7   5
  17P LOSS WILD-TYPE 199 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7    5
  17P LOSS WILD-TYPE  199  261
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                7                199
  MALE                  5                261
[1] 2 2
[1] FALSE
D70V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17P LOSS MUTATED             6                2                 4
  17P LOSS WILD-TYPE         170              116               174
D70V5, multiclass
                   clus
vv                  17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASTROCYTOMA                      6                170
  OLIGOASTROCYTOMA                 2                116
  OLIGODENDROGLIOMA                4                174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1  11
  17P LOSS WILD-TYPE  91 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   11
  17P LOSS WILD-TYPE   91  369
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 1                 91
  YES               11                369
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     0
  17P LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           0    12
  17P LOSS WILD-TYPE                        15   425
D70V7, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          12                425
[1] 4 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, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     2  10
  17P LOSS WILD-TYPE  16 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2   10
  17P LOSS WILD-TYPE   16  409
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               10                409
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     7   1
  17Q LOSS WILD-TYPE 369  93
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                462 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 93 
$`17Q LOSS MUTATED`
TCGA-DU-6400 TCGA-DU-8165 TCGA-FG-A4MY TCGA-HT-7689 TCGA-HT-8106 TCGA-HT-8564 
        1.22        19.13        23.70        14.96         0.10        15.72 
TCGA-P5-A5EZ TCGA-P5-A5F6 
        2.30         1.28 

$`17Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        5.10        23.74        14.60        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.38        18.71        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       31.69         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         6.25         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV 
        0.23        29.59        34.19        28.27         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         5.88         7.63         0.76         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             23.70             211.17 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              8.63              18.74 
[1] "0.1 - 23.7 (8.6)"   "0.0 - 211.2 (18.7)"
[1] "hr=" "2.4"
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4   4
  17Q LOSS WILD-TYPE 202 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    4
  17Q LOSS WILD-TYPE  202  262
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                4                202
  MALE                  4                262
[1] 2 2
[1] FALSE
D71V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17Q LOSS MUTATED             3                1                 4
  17Q LOSS WILD-TYPE         173              117               174
D71V5, multiclass
                   clus
vv                  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASTROCYTOMA                      3                173
  OLIGOASTROCYTOMA                 1                117
  OLIGODENDROGLIOMA                4                174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1   7
  17Q LOSS WILD-TYPE  91 373
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    7
  17Q LOSS WILD-TYPE   91  373
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                 91
  YES                7                373
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     0
  17Q LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           0     8
  17Q LOSS WILD-TYPE                        15   429
D71V7, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                           8                429
[1] 4 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, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2   6
  17Q LOSS WILD-TYPE  16 413
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    6
  17Q LOSS WILD-TYPE   16  413
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO                6                413
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    49  14
  18P LOSS WILD-TYPE 327  80
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                63                407 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                14                 80 
$`18P LOSS MUTATED`
TCGA-CS-4943 TCGA-CS-5396 TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-A4XD TCGA-DB-A4XG 
       18.15         9.96        47.93        44.52        39.78        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A66B 
       31.63        24.20        19.96        30.31        30.21        42.05 
TCGA-DU-5849 TCGA-DU-6393 TCGA-DU-6407 TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7300 
       14.56        52.11        94.52       138.28       117.40        62.01 
TCGA-DU-8158 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A7T6 TCGA-E1-5307 TCGA-FG-8188 
        5.10        12.59         4.96        17.98        57.93        14.96 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7688 
        6.54        24.26        75.19        45.99         0.23        31.69 
TCGA-HT-7692 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-8564 TCGA-HT-A5RB TCGA-HT-A616 
        2.96         0.23        50.63        15.72         0.10         1.81 
TCGA-HT-A617 TCGA-HT-A74L TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-A5KK TCGA-P5-A5EX 
       16.14        11.05        40.18        21.60        12.76         1.64 
TCGA-P5-A5EZ TCGA-P5-A72Z TCGA-QH-A65R TCGA-QH-A65Z TCGA-RY-A840 TCGA-S9-A6TS 
        2.30        11.64        15.16        14.04        28.08        62.17 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6UA TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A6WL 
       37.84        34.49         5.85        69.50        32.45        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-S9-A89V 
       19.86        15.91        15.16        28.37        10.39        18.71 
TCGA-TM-A84G TCGA-TM-A84I TCGA-VM-A8CA 
       40.64        28.08        13.51 

$`18P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10        21.01         6.38        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       12.43         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
      122.73        81.96        75.25        72.92        50.86        50.17 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       37.45        33.57        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 
       11.24        17.88        30.74        16.18        31.82        14.40 
TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
        8.02        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
       13.38         3.45        18.61        18.02        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16       211.17        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       19.89        16.83       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       18.94        44.02        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        2.76        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TU 
       16.96        15.48        14.17        14.24        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        41.13        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        20.09        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 
        0.03        16.54         3.75        17.42         6.38        40.34 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       56.09        57.60        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 
       44.68         6.05        42.74         0.10        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       39.09         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
        5.33         2.70        16.93        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7486 
       17.65         2.43        10.52        15.35         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        35.90         4.31        21.70 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       19.59        17.82        20.35        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY 
       42.77        14.40        14.40         0.23         6.71         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65S 
       10.42        13.25         0.20         9.01        13.61         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       12.62        15.85        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV 
        9.90         2.07        19.59        30.67        87.12        18.77 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG 
       16.08        98.24        95.93       106.39        72.59        80.12 
TCGA-S9-A6WI TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       84.99        18.61        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 
       15.06        13.12        13.02       169.84        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        31.59        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H 
       34.78        48.39        24.92        16.18        59.05        30.44 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.10               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            138.28             211.17 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             21.60              18.51 
[1] "0.1 - 138.3 (21.6)" "0.0 - 211.2 (18.5)"
[1] "hr=" "1.1"
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    22  41
  18P LOSS WILD-TYPE 184 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     22   41
  18P LOSS WILD-TYPE  184  225
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               22                184
  MALE                 41                225
[1] 2 2
[1] FALSE
D72V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18P LOSS MUTATED            24               11                28
  18P LOSS WILD-TYPE         152              107               150
D72V5, multiclass
                   clus
vv                  18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASTROCYTOMA                     24                152
  OLIGOASTROCYTOMA                11                107
  OLIGODENDROGLIOMA               28                150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    11  52
  18P LOSS WILD-TYPE  81 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     11   52
  18P LOSS WILD-TYPE   81  328
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                11                 81
  YES               52                328
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  1     0
  18P LOSS WILD-TYPE                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           0    59
  18P LOSS WILD-TYPE                        15   378
D72V7, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          59                378
[1] 4 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, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  53
  18P LOSS WILD-TYPE  15 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   53
  18P LOSS WILD-TYPE   15  366
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 15
  NOT HISPANIC OR LATINO               53                366
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    46  12
  18Q LOSS WILD-TYPE 330  82
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                58                412 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                12                 82 
$`18Q LOSS MUTATED`
TCGA-CS-5396 TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A4XH 
        9.96        47.93        44.52        39.78        72.95        31.63 
TCGA-DB-A64L TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A7UT 
       24.20        19.96        30.31        30.21        42.05        13.38 
TCGA-DU-5849 TCGA-DU-5870 TCGA-DU-6393 TCGA-DU-6407 TCGA-DU-7009 TCGA-DU-7014 
       14.56       182.33        52.11        94.52       138.28       117.40 
TCGA-DU-7300 TCGA-DU-8158 TCGA-DU-A5TT TCGA-DU-A7T6 TCGA-E1-5307 TCGA-FG-8188 
       62.01         5.10         4.96        17.98        57.93        14.96 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7616 
        6.54        24.26        75.19        17.29        45.99         0.23 
TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7857 TCGA-HT-8564 TCGA-HT-A5RB TCGA-HT-A617 
       31.69         2.96         0.23        15.72         0.10        16.14 
TCGA-HT-A74L TCGA-HW-7491 TCGA-HW-8320 TCGA-P5-A5EX TCGA-P5-A72Z TCGA-QH-A65R 
       11.05        40.18        21.60         1.64        11.64        15.16 
TCGA-QH-A65Z TCGA-RY-A840 TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6WD 
       14.04        28.08        62.17        37.84        34.49        69.50 
TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7QY 
       32.45        31.10        19.86        15.91        15.16        28.37 
TCGA-S9-A7R2 TCGA-TM-A84G TCGA-TM-A84I TCGA-VM-A8CA 
       10.39        40.64        28.08        13.51 

$`18Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 
        6.61       122.73        81.96        75.25        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       46.72        37.45        33.57        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 
       12.10        11.24        17.88        30.74        16.18        31.82 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       14.40         8.02        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
       13.12         3.45        18.61        18.02        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45         6.81        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
      211.17        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        41.13        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        20.09        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 
        0.03        16.54         3.75        17.42         6.38        40.34 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 
       23.18       122.47         4.57         3.16        22.06        56.09 
TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 
        5.33         2.70        16.93         1.81        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74O 
       17.52        17.65         2.43        10.52        15.35         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.70        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        6.71         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 
        0.76         1.28         0.16        10.42        13.25         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS 
        9.01        13.61         2.53        12.62        15.85        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 
       59.38        30.87         5.46         9.90         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       30.67        87.12        18.77        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WO 
        5.85       106.39        72.59        80.12        84.99        18.61 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02       169.84        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84J 
       48.39        24.92        16.18        59.05        30.44        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB 
       23.80        15.98        26.99        43.04        30.08         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.10               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            182.33             211.17 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             26.17              18.41 
[1] "0.1 - 182.3 (26.2)" "0.0 - 211.2 (18.4)"
[1] "hr=" "1.2"
D73V2, continuous
D73V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    23  35
  18Q LOSS WILD-TYPE 183 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     23   35
  18Q LOSS WILD-TYPE  183  231
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               23                183
  MALE                 35                231
[1] 2 2
[1] FALSE
D73V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18Q LOSS MUTATED            19               10                29
  18Q LOSS WILD-TYPE         157              108               149
D73V5, multiclass
                   clus
vv                  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASTROCYTOMA                     19                157
  OLIGOASTROCYTOMA                10                108
  OLIGODENDROGLIOMA               29                149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    11  47
  18Q LOSS WILD-TYPE  81 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     11   47
  18Q LOSS WILD-TYPE   81  333
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                11                 81
  YES               47                333
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  1     0
  18Q LOSS WILD-TYPE                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           0    54
  18Q LOSS WILD-TYPE                        15   383
D73V7, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          54                383
[1] 4 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, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3  50
  18Q LOSS WILD-TYPE  15 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   50
  18Q LOSS WILD-TYPE   15  369
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 15
  NOT HISPANIC OR LATINO               50                369
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    17   5
  19P LOSS WILD-TYPE 359  89
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                448 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 89 
$`19P LOSS MUTATED`
TCGA-CS-4942 TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A66B 
       43.89        50.86        19.96        30.31         8.02        42.05 
TCGA-DU-5855 TCGA-DU-A5TS TCGA-E1-5318 TCGA-HT-7688 TCGA-HT-7857 TCGA-HT-8111 
        6.81        15.12        78.21        31.69         0.23         0.23 
TCGA-HT-8564 TCGA-P5-A5F6 TCGA-R8-A6MO TCGA-RY-A840 TCGA-S9-A6TX TCGA-S9-A6WI 
       15.72         1.28        32.65        28.08        34.49        84.99 
TCGA-S9-A7IS TCGA-TM-A84M TCGA-TQ-A7RH TCGA-WY-A858 
        7.92        24.79        15.98        43.96 

$`19P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 
       11.24        17.88        30.74        16.18        31.82        14.40 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
        6.74        13.38         8.45       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT 
       16.96        15.48        14.17        14.24        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
       57.93       134.27        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        19.23        39.09        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        28.27         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         5.88         7.63         0.76         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A73M TCGA-RY-A83X 
       11.08        12.99        88.83        94.03        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        5.46         9.90         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       87.12        18.77        37.84        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
       36.13        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       28.08        24.16        40.83        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       14.93        23.80        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A 
       23.21         8.05        51.06        13.32        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.23               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             84.99             211.17 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            26.435             18.610 
[1] "0.2 - 85.0 (26.4)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.2"
D74V2, continuous
D74V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    10  12
  19P LOSS WILD-TYPE 196 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     10   12
  19P LOSS WILD-TYPE  196  254
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               10                196
  MALE                 12                254
[1] 2 2
[1] FALSE
D74V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19P LOSS MUTATED             8                5                 9
  19P LOSS WILD-TYPE         168              113               169
D74V5, multiclass
                   clus
vv                  19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASTROCYTOMA                      8                168
  OLIGOASTROCYTOMA                 5                113
  OLIGODENDROGLIOMA                9                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     7  15
  19P LOSS WILD-TYPE  85 365
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7   15
  19P LOSS WILD-TYPE   85  365
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 7                 85
  YES               15                365
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     1
  19P LOSS WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           2    17
  19P LOSS WILD-TYPE                        13   420
D74V7, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          17                420
[1] 4 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, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2  16
  19P LOSS WILD-TYPE  16 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   16
  19P LOSS WILD-TYPE   16  403
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               16                403
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED   161  31
  19Q LOSS WILD-TYPE 215  63
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               192                278 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                31                 63 
$`19Q LOSS MUTATED`
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 
       43.89        18.15        64.64         9.96         8.02         6.61 
TCGA-DB-5274 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG 
       75.25        50.86        50.17        44.52        18.84        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U 
       31.63        24.20        30.12         5.98        31.40        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-5141 
       29.23        14.40        12.10        11.24        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5855 TCGA-DU-5870 
       17.19        54.25        13.12        14.56         6.81       182.33 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6408 
       15.16        52.11        22.42        46.06         1.22       114.08 
TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7298 
        7.96       138.28       117.40        30.67        94.32        18.94 
TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S2 
       62.01        60.30        21.40        14.17        15.12         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TC 
        2.70        77.98         5.98        21.30        17.98        23.51 
TCGA-DU-A7TG TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       44.42        41.13        79.99       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 
      130.78        75.02        14.33         0.23        47.77        34.36 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8186 TCGA-FG-8187 
       15.35        17.88        22.55        20.61        16.01        20.09 
TCGA-FG-8188 TCGA-FG-A4MT TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 
       14.96        38.27        17.82        15.02        16.44        36.66 
TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7480 
       20.45         0.10         6.67        11.54         0.13        75.19 
TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 
       95.93         4.57         3.16        22.06         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7694 
       16.24        44.68         0.10        31.69         2.96         6.90 
TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       14.53        39.09         0.23        37.15         0.33         0.13 
TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8111 
       35.47         1.64         9.40         6.25         5.56         0.23 
TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A619 TCGA-HT-A61B 
       15.72        26.04         0.07        16.93        21.40        17.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 
       15.35        11.05        29.92        19.89        40.18         4.31 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 
       17.82        20.35        42.77        14.40         1.64         4.11 
TCGA-P5-A5F6 TCGA-P5-A72Z TCGA-P5-A730 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
        1.28        11.64         0.20        15.16        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.04        14.83         2.20         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       16.73        11.08        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 TCGA-S9-A6TW TCGA-S9-A6TX 
       30.87         5.46        28.08        30.67        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       31.33        23.64        32.61       106.39        69.50        72.59 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IQ 
       32.45        84.99        31.10        15.91        15.16        36.13 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY 
        7.92        23.51         8.19         2.04        17.03        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O 
       13.02       169.84        49.32        40.64        24.79        33.24 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CA 
       18.61        14.93        15.98        26.99        43.04        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 TCGA-WY-A858 
        0.10        35.93        37.05        23.21        51.06        43.96 

$`19Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 
        4.70         7.69        10.62        40.18         0.10        21.01 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
        6.38        17.69        23.84        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.56         7.40       122.73        81.96        47.93        72.92 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        78.28        46.42        30.21        46.72        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75M 
       37.45        33.57        25.48        27.45        18.51        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5143 TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       30.74        16.18        14.40        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5871 
       18.02        17.46         6.74        13.38         8.45        18.94 
TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 
       17.49       211.17        49.02        75.16        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 
        7.73        11.47        62.96       156.23        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        6.54         8.84        90.77        26.30        10.36         7.96 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       44.02        25.91        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59         4.96         3.65         5.65        12.20 
TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TA 
        7.23        11.41        26.76         7.13       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5307 
       42.31         7.50         0.56        50.14        67.46        57.93 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 
       32.45        36.82        32.35         0.20        25.48        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7643 
       18.77        14.93        24.99        23.97        18.44        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU 
       12.95        13.68        14.24        22.52        32.61        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 
       18.38        18.71        23.70        14.76        16.41        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       28.54        10.78        48.69        13.58         5.72        27.52 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       40.11         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       24.26         6.38        40.34       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 
        5.03        29.85        23.18       122.47        17.29        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 
       56.09        57.60         0.16         0.76         6.05        42.74 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 
       14.96         0.10         0.10        17.52        39.48        19.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 
       50.63         0.49        23.61         3.68         5.33         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
       11.28        31.43        16.24        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 
       33.01        12.23         0.10         0.46         2.50        13.78 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R7 
       29.59        34.19        28.27         0.23         0.13        20.22 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 
       27.35         0.10         5.33         2.70         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7489 
       16.83        17.65         2.43        10.52         0.10         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK 
       19.23        35.90        21.70        21.60        19.59        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.81        20.71        19.00        14.40         0.23         6.71 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U 
        2.37         2.30         5.88         7.63         0.76         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65S TCGA-QH-A6CS 
       10.42        13.25         9.01        13.61         2.53        19.33 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA 
       14.53        13.61        12.23        10.29         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A870 TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS 
        5.03        12.99         9.90         2.07        19.59        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U6 
       87.12        18.77        28.70        22.95        17.62        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO 
       98.24        95.93         5.85        80.12        19.86        18.61 
TCGA-S9-A6WQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX 
       14.07        22.32         7.13        20.02        15.06        13.12 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       11.97        49.45        48.33        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        30.44        28.08        24.16        40.83 
TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH TCGA-VV-A86M 
       25.38        23.80        30.08         7.89        23.47        16.01 
TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
        8.05        13.32        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            182.33             211.17 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             20.22              18.20 
[1] "0.1 - 182.3 (20.2)" "0.0 - 211.2 (18.2)"
[1] "hr=" "1.7"
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    85 108
  19Q LOSS WILD-TYPE 121 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     85  108
  19Q LOSS WILD-TYPE  121  158
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               85                121
  MALE                108                158
[1] 2 2
[1] FALSE
D75V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19Q LOSS MUTATED            21               38               134
  19Q LOSS WILD-TYPE         155               80                44
D75V5, multiclass
                   clus
vv                  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASTROCYTOMA                     21                155
  OLIGOASTROCYTOMA                38                 80
  OLIGODENDROGLIOMA              134                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    31 162
  19Q LOSS WILD-TYPE  61 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     31  162
  19Q LOSS WILD-TYPE   61  218
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                31                 61
  YES              162                218
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     4
  19Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           6   176
  19Q LOSS WILD-TYPE                         9   261
D75V7, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  4
  BLACK OR AFRICAN AMERICAN                       6                  9
  WHITE                                         176                261
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     9 169
  19Q LOSS WILD-TYPE   9 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      9  169
  19Q LOSS WILD-TYPE    9  250
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                  9
  NOT HISPANIC OR LATINO              169                250
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     4   1
  20P LOSS WILD-TYPE 372  93
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                465 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 93 
$`20P LOSS MUTATED`
TCGA-DB-5277 TCGA-DU-8166 TCGA-FG-A87N TCGA-HT-7693 TCGA-S9-A89V 
       50.86        16.96        13.58        17.52        18.71 

$`20P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       48.69        20.45         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 
       31.69        14.96         0.10         0.10         2.96         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        31.59        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             13.58               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             50.86             211.17 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             17.52              18.71 
[1] "13.6 - 50.9 (17.5)" "0.0 - 211.2 (18.7)"
[1] "hr=" "1.3"
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3   2
  20P LOSS WILD-TYPE 203 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    2
  20P LOSS WILD-TYPE  203  264
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                203
  MALE                  2                264
[1] 2 2
[1] FALSE
D76V4, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                267 
        TCGA-CS-4938         TCGA-CS-4941         TCGA-CS-4942 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-4943         TCGA-CS-4944         TCGA-CS-5390 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5393         TCGA-CS-5395         TCGA-CS-5396 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5397         TCGA-CS-6186         TCGA-CS-6188 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-6290         TCGA-CS-6665         TCGA-CS-6666 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-6667         TCGA-CS-6668         TCGA-CS-6669 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-A4XE         TCGA-DB-A64L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-A64Q         TCGA-DB-A64R         TCGA-DB-A64S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-A64U         TCGA-DB-A64V         TCGA-DB-A64W 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-A64X         TCGA-DB-A75L         TCGA-DB-A75O 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5142         TCGA-DH-5143 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-DH-A66B         TCGA-DH-A66D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-A66F         TCGA-DH-A66G         TCGA-DH-A7UR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-A7UU         TCGA-DH-A7UV         TCGA-DU-5851 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-5852         TCGA-DU-5853         TCGA-DU-5854 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-5855         TCGA-DU-5870         TCGA-DU-5871 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-5874         TCGA-DU-6396         TCGA-DU-6403 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-6404         TCGA-DU-6405         TCGA-DU-6407 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-6408         TCGA-DU-6410         TCGA-DU-7011 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7013         TCGA-DU-7014         TCGA-DU-7015 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7018         TCGA-DU-7019         TCGA-DU-7294 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7298         TCGA-DU-7299         TCGA-DU-7300 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7301         TCGA-DU-7302         TCGA-DU-7304 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7306         TCGA-DU-7309         TCGA-DU-8158 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-8161         TCGA-DU-8162         TCGA-DU-8163 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-8165         TCGA-DU-8167         TCGA-DU-8168 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A5TP         TCGA-DU-A5TR         TCGA-DU-A5TS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A5TU         TCGA-DU-A5TW         TCGA-DU-A6S2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A6S6         TCGA-DU-A6S7         TCGA-DU-A6S8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A76R         TCGA-DU-A7T6         TCGA-DU-A7T8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A7TA         TCGA-DU-A7TB         TCGA-DU-A7TC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A7TD         TCGA-DU-A7TG         TCGA-E1-5302 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5305 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5307         TCGA-E1-5311         TCGA-E1-5318 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5319         TCGA-E1-5322         TCGA-E1-A7YO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-A7YV         TCGA-E1-A7YW         TCGA-E1-A7Z6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-5963         TCGA-FG-5965         TCGA-FG-6688 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-6689         TCGA-FG-6690         TCGA-FG-6691 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-7636         TCGA-FG-7638         TCGA-FG-8181 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-8185         TCGA-FG-8186         TCGA-FG-8187 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-8188         TCGA-FG-8189         TCGA-FG-A4MT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-A4MW         TCGA-FG-A4MX         TCGA-FG-A60J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-A60L         TCGA-FG-A6J1         TCGA-FG-A6J3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-A711         TCGA-FG-A713         TCGA-FG-A87Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7468         TCGA-HT-7470         TCGA-HT-7475 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7477         TCGA-HT-7485         TCGA-HT-7607 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7609         TCGA-HT-7611         TCGA-HT-7689 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7692         TCGA-HT-7694         TCGA-HT-7854 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7875         TCGA-HT-7884         TCGA-HT-8564 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-A4DV         TCGA-HT-A5R7         TCGA-HT-A5RA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-A5RC         TCGA-HT-A615         TCGA-HT-A617 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-A618         TCGA-HT-A61B         TCGA-HT-A61C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-A74L         TCGA-IK-7675         TCGA-KT-A74X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KT-A7W1         TCGA-P5-A5EU         TCGA-P5-A5EV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-P5-A5EW         TCGA-P5-A5EX         TCGA-P5-A5F0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-P5-A5F2         TCGA-P5-A5F4         TCGA-P5-A5F6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-P5-A731         TCGA-QH-A65R         TCGA-QH-A65S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A65V         TCGA-QH-A65X         TCGA-QH-A65Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6CS         TCGA-QH-A6CU         TCGA-QH-A6CV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6CW         TCGA-QH-A6CX         TCGA-QH-A6CY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6CZ         TCGA-QH-A6X3         TCGA-QH-A6X4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6X5         TCGA-QH-A6X8         TCGA-QH-A6X9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6XA         TCGA-QH-A6XC         TCGA-QH-A86X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A870         TCGA-RY-A83Y         TCGA-RY-A840 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-RY-A845         TCGA-RY-A847         TCGA-S9-A6TS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6TU         TCGA-S9-A6TV         TCGA-S9-A6TW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6TX         TCGA-S9-A6TY         TCGA-S9-A6TZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6U0         TCGA-S9-A6U1         TCGA-S9-A6U2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6U5         TCGA-S9-A6U6         TCGA-S9-A6U8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6UA         TCGA-S9-A6UB         TCGA-S9-A6WD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WE         TCGA-S9-A6WG         TCGA-S9-A6WH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WI         TCGA-S9-A6WL         TCGA-S9-A6WM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WN         TCGA-S9-A6WO         TCGA-S9-A6WP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WQ         TCGA-S9-A7IQ         TCGA-S9-A7IS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7IX         TCGA-S9-A7IY         TCGA-S9-A7IZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7J0         TCGA-S9-A7J1         TCGA-S9-A7J2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7J3         TCGA-S9-A7QW         TCGA-S9-A7QX 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7QY         TCGA-S9-A7QZ         TCGA-S9-A7R1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7R2         TCGA-S9-A7R3         TCGA-S9-A7R4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7R7         TCGA-S9-A7R8         TCGA-S9-A89Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A7C3         TCGA-TM-A7C4         TCGA-TM-A7C5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A7CA         TCGA-TM-A7CF         TCGA-TM-A84B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84C         TCGA-TM-A84F         TCGA-TM-A84G 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84H         TCGA-TM-A84I         TCGA-TM-A84J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84L         TCGA-TM-A84M         TCGA-TM-A84O 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84Q         TCGA-TM-A84R         TCGA-TM-A84S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84T         TCGA-TQ-A7RW         TCGA-VM-A8C8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-VM-A8CA         TCGA-VM-A8CD         TCGA-VM-A8CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-VM-A8CH         TCGA-WY-A858         TCGA-WY-A859 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20P LOSS MUTATED             3                1                 1
  20P LOSS WILD-TYPE         173              117               177
D76V5, multiclass
                   clus
vv                  20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASTROCYTOMA                      3                173
  OLIGOASTROCYTOMA                 1                117
  OLIGODENDROGLIOMA                1                177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2   3
  20P LOSS WILD-TYPE  90 377
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    3
  20P LOSS WILD-TYPE   90  377
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 2                 90
  YES                3                377
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     1
  20P LOSS WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           0     4
  20P LOSS WILD-TYPE                        15   433
D76V7, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  7
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                           4                433
[1] 4 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, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0   5
  20P LOSS WILD-TYPE  18 414
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    5
  20P LOSS WILD-TYPE   18  414
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO                5                414
[1] 2 2
[1] FALSE

Clustering(77) Variable = 21Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    26   3
  21Q LOSS WILD-TYPE 350  91
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                441 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 91 
$`21Q LOSS MUTATED`
TCGA-CS-4943 TCGA-DB-5279 TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-5142 TCGA-DU-5871 
       18.15        44.52        11.24        19.96        30.31        18.94 
TCGA-DU-7010 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TU TCGA-DU-A7TA TCGA-E1-5307 
       14.99        19.13        15.48         3.65        77.88        57.93 
TCGA-FG-7636 TCGA-FG-A60J TCGA-HT-7689 TCGA-HT-7857 TCGA-HT-7902 TCGA-HT-8106 
       17.88        14.76        14.96         0.23        31.43         0.10 
TCGA-HT-8564 TCGA-HT-A61B TCGA-HW-7490 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ 
       15.72        17.52        19.23         0.23         6.71         2.30 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-S9-A89Z TCGA-TM-A84Q 
        0.76         1.28        10.42        11.97        25.38 

$`21Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.86        50.17        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 
       17.88        30.74        16.18        31.82        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       30.21        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       13.12        13.38         3.45        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        5.10        23.74        14.60        20.68        21.40        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         4.96         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        41.13        79.99       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L 
       10.72        18.38        18.71        23.70        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        31.69         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 
        6.90        14.53        39.48        19.23        39.09        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47         3.72        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        28.27         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C 
       16.93         1.81        16.14        16.83        21.40        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EX 
       20.71        19.00        42.77        14.40        14.40         1.64 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A72U TCGA-P5-A72X 
        2.37         4.11         5.88         7.63         0.16        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 
       99.06        30.05        98.63        31.59        18.71        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       24.79        33.24        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             77.88             211.17 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             15.48              18.84 
[1] "0.1 - 77.9 (15.5)"  "0.0 - 211.2 (18.8)"
[1] "hr=" "1.1"
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    14  15
  21Q LOSS WILD-TYPE 192 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     14   15
  21Q LOSS WILD-TYPE  192  251
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               14                192
  MALE                 15                251
[1] 2 2
[1] FALSE
D77V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  21Q LOSS MUTATED            18                5                 6
  21Q LOSS WILD-TYPE         158              113               172
D77V5, multiclass
                   clus
vv                  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASTROCYTOMA                     18                158
  OLIGOASTROCYTOMA                 5                113
  OLIGODENDROGLIOMA                6                172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4  25
  21Q LOSS WILD-TYPE  88 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   25
  21Q LOSS WILD-TYPE   88  355
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                 88
  YES               25                355
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     0
  21Q LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           0    28
  21Q LOSS WILD-TYPE                        15   409
D77V7, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          28                409
[1] 4 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, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  26
  21Q LOSS WILD-TYPE  17 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   26
  21Q LOSS WILD-TYPE   17  393
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               26                393
[1] 2 2
[1] FALSE

Clustering(78) Variable = 22Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    30  20
  22Q LOSS WILD-TYPE 346  74
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                50                420 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                20                 74 
$`22Q LOSS MUTATED`
TCGA-CS-4943 TCGA-CS-5397 TCGA-CS-6186 TCGA-DB-5277 TCGA-DB-A64L TCGA-DB-A64O 
       18.15         6.38        17.69        50.86        24.20        25.48 
TCGA-DH-A669 TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-6399 TCGA-DU-7008 
       30.21        18.02         6.74        13.38        65.75       156.23 
TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-8167 
       10.36        18.94         5.10        23.74        19.13        15.48 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-E1-5304 
        4.96         3.65        12.20        11.41        26.76        41.13 
TCGA-E1-5322 TCGA-FG-7643 TCGA-FG-A4MY TCGA-HT-7477 TCGA-HT-7686 TCGA-HT-7688 
      130.78        20.09        23.70        24.26        42.74        31.69 
TCGA-HT-7690 TCGA-HT-7860 TCGA-HT-A614 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-A5KK 
        0.10         0.49         2.70        16.14        16.83        12.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-QH-A6CS TCGA-RY-A83Z TCGA-S9-A6TS TCGA-S9-A6UA 
        1.28         0.16        19.33         9.90        62.17         5.85 
TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A84G TCGA-TQ-A7RW 
       22.32        20.02        18.71        11.97        40.64        26.99 
TCGA-VM-A8CD TCGA-WH-A86K 
        7.89        13.32 

$`22Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
        0.10        21.01         9.96        23.84        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
        8.48         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P 
       39.78        37.45        33.57        72.95        31.63        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5854 TCGA-DU-5855 
        3.45        18.61        14.56        17.46         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 
       22.42        49.02        75.16        46.06         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7009 
      114.08         7.96         7.73        11.47        62.96       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 
       30.67        26.30         7.96        94.32        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 
       25.91        60.30        23.31        41.98         2.76        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       20.68        21.40        16.96        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       15.12         5.65         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
        5.98         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       22.55        20.61        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.38        18.71        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7691 
        0.76        44.68         6.05         0.10        14.96         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23        50.63        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 
        0.07        27.35         0.10         5.33        16.93         1.81 
TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       21.40        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       17.82        20.35        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72W 
        2.30         4.11         5.88         7.63         0.76        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        15.85        14.04        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU 
        5.46        28.08         2.07        19.59        30.67        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
       36.13         7.92        23.51         7.13         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 
       10.39        99.06        30.05        98.63        31.59        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       59.05        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       43.04        30.08        13.51         0.10        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 
       37.05        16.01        23.21         8.05        51.06        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.10               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            156.23             211.17 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            18.085             18.740 
[1] "0.1 - 156.2 (18.1)" "0.0 - 211.2 (18.7)"
[1] "hr=" "2.8"
D78V2, continuous
D78V3, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    24  26
  22Q LOSS WILD-TYPE 182 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24   26
  22Q LOSS WILD-TYPE  182  240
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               24                182
  MALE                 26                240
[1] 2 2
[1] FALSE
D78V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  22Q LOSS MUTATED            24               11                15
  22Q LOSS WILD-TYPE         152              107               163
D78V5, multiclass
                   clus
vv                  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASTROCYTOMA                     24                152
  OLIGOASTROCYTOMA                11                107
  OLIGODENDROGLIOMA               15                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     9  41
  22Q LOSS WILD-TYPE  83 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   41
  22Q LOSS WILD-TYPE   83  339
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 9                 83
  YES               41                339
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     0
  22Q LOSS WILD-TYPE                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           1    48
  22Q LOSS WILD-TYPE                        14   389
D78V7, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          48                389
[1] 4 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, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     2  44
  22Q LOSS WILD-TYPE  16 375
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   44
  22Q LOSS WILD-TYPE   16  375
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               44                375
[1] 2 2
[1] FALSE

Clustering(79) Variable = XP LOSS MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    65  23
  XP LOSS WILD-TYPE 311  71
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               88               382 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               23                71 
$`XP LOSS MUTATED`
TCGA-CS-4938 TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XH TCGA-DB-A64W 
        4.70        47.93        44.52        78.28        31.63        14.40 
TCGA-DH-5140 TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5871 TCGA-DU-6401 TCGA-DU-6404 
       19.96         3.45        18.02        18.94        87.45       133.74 
TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
       94.52         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8168 
       30.67        94.32        44.02        60.30         5.10        14.17 
TCGA-DU-A5TS TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-E1-5307 TCGA-E1-5311 
       15.12         5.98        21.30        17.98        57.93       134.27 
TCGA-E1-5322 TCGA-E1-A7YV TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5964 TCGA-FG-7636 
      130.78        32.45        14.33         0.23        34.36        17.88 
TCGA-FG-A4MY TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A713 TCGA-HT-7469 TCGA-HT-7471 
       23.70        15.02        16.44        20.45        11.54         0.13 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7689 TCGA-HT-7690 
        6.54        24.26        45.99         0.23        14.96         0.10 
TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7902 TCGA-HT-8104 TCGA-HT-8563 
        2.96        19.23         0.23        31.43        12.23        28.27 
TCGA-HT-8564 TCGA-HT-A618 TCGA-HT-A61B TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-8321 
       15.72        16.83        17.52        40.18        21.60        19.59 
TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72Z 
       19.00        14.40         2.30         1.28        10.42        11.64 
TCGA-QH-A65S TCGA-QH-A65Z TCGA-QH-A6X4 TCGA-QH-A6X8 TCGA-RY-A83Z TCGA-S9-A6TS 
        2.53        14.04        14.53        16.73         9.90        62.17 
TCGA-S9-A6TV TCGA-S9-A6U1 TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A89V 
       18.77        17.62        15.16         7.92         7.13        18.71 
TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A84I TCGA-TM-A84Q TCGA-TQ-A7RW TCGA-VM-A8CD 
       11.97        49.32        28.08        25.38        26.99         7.89 
TCGA-VV-A829 TCGA-VV-A86M TCGA-WY-A858 TCGA-WY-A85B 
       37.05        16.01        43.96        45.80 

$`XP LOSS WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        7.69        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 
        6.61       122.73        81.96        75.25        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       50.17        36.56        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O 
       39.78        37.45        33.57        72.95        24.20        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.61        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-7009 
        7.04        11.64        19.89        16.83       114.08       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 
       26.30        10.36         7.96        18.94        62.01        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         2.76        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        19.13        16.96        15.48        14.24        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 
       77.98         7.23        11.41        26.76         7.13       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5318 TCGA-E1-5319 
       50.14        67.46        41.13        79.99        78.21        95.57 
TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       75.02        36.82        32.35         0.20        47.77        25.48 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       15.35        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K 
       38.27        10.72        18.38        18.71        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.41        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
       13.58         5.72        27.52         0.10         6.67        40.11 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 
        0.03        16.54         3.75        17.42         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       22.06        56.09        57.60        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        0.10        17.52         6.90        14.53        39.48        39.09 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 
        3.68         5.33        35.47         3.72        11.28         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        0.23        29.59        34.19         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H 
       16.93         1.81        16.14        21.40        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8322 
        8.32        19.23        35.90         4.31        21.70        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A7W1 
       20.35        12.76        20.81        20.71        42.77        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 
        7.63         0.76         0.16        13.25         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU 
       13.61        15.16        12.62        15.85        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TW 
       28.08         2.07        19.59        30.67        87.12        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 
       34.49        31.33        28.70        22.95        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY 
       15.91        18.61        14.07        36.13        22.32        23.51 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF 
       98.63        31.59        49.45        48.33        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       24.92        16.18        59.05        40.64        30.44        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        24.79        33.24        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       15.98        43.04        30.08        13.51         0.10        35.93 
TCGA-VM-A8CH TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A859 
       23.47        23.21         8.05        51.06        13.32        39.88 
TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        46.88        37.71        20.81 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.10              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           156.23            211.17 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           17.930            18.805 
[1] "0.1 - 156.2 (17.9)" "0.0 - 211.2 (18.8)"
[1] "hr=" "1.4"
D79V2, continuous
D79V3, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    42  47
  XP LOSS WILD-TYPE 164 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     42   47
  XP LOSS WILD-TYPE  164  219
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              42               164
  MALE                47               219
[1] 2 2
[1] FALSE
D79V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XP LOSS MUTATED            36               22                31
  XP LOSS WILD-TYPE         140               96               147
D79V5, multiclass
                   clus
vv                  XP LOSS MUTATED XP LOSS WILD-TYPE
  ASTROCYTOMA                    36               140
  OLIGOASTROCYTOMA               22                96
  OLIGODENDROGLIOMA              31               147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    17  72
  XP LOSS WILD-TYPE  75 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     17   72
  XP LOSS WILD-TYPE   75  308
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               17                75
  YES              72               308
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0     1
  XP LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                           1    85
  XP LOSS WILD-TYPE                        14   352
D79V7, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         85               352
[1] 4 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, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     6  78
  XP LOSS WILD-TYPE  12 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      6   78
  XP LOSS WILD-TYPE   12  341
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                12
  NOT HISPANIC OR LATINO              78               341
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    45  19
  XQ LOSS WILD-TYPE 331  75
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               64               406 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               19                75 
$`XQ LOSS MUTATED`
TCGA-CS-6667 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XH TCGA-DB-A64W 
        7.56        47.93        50.86        44.52        31.63        14.40 
TCGA-DH-5140 TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-6404 TCGA-DU-6410 TCGA-DU-6542 
       19.96        17.19        18.02       133.74         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-8158 
       11.47        30.67        94.32        44.02        60.30         5.10 
TCGA-DU-8168 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-E1-5302 TCGA-E1-5311 
       14.17         5.98        21.30        17.98        50.14       134.27 
TCGA-E1-A7YV TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5964 TCGA-FG-A6IZ TCGA-FG-A6J1 
       32.45        14.33         0.23        34.36        15.02        16.44 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7477 TCGA-HT-7616 TCGA-HT-7690 TCGA-HT-7692 
       11.54         0.13        24.26         0.23         0.10         2.96 
TCGA-HT-7855 TCGA-HT-8104 TCGA-HT-8564 TCGA-HT-A61B TCGA-HW-7491 TCGA-HW-7493 
       19.23        12.23        15.72        17.52        40.18        35.90 
TCGA-HW-8321 TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-P5-A5F6 TCGA-P5-A72W 
       19.59        19.00        14.40         2.30         1.28        10.42 
TCGA-P5-A72Z TCGA-QH-A65Z TCGA-QH-A6X4 TCGA-QH-A6X8 TCGA-RY-A83Z TCGA-S9-A6TV 
       11.64        14.04        14.53        16.73         9.90        18.77 
TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7QW TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C5 
       15.16         7.92        15.06        18.71        11.97        49.32 
TCGA-TM-A84I TCGA-TQ-A7RW TCGA-VM-A8CD TCGA-VV-A829 
       28.08        26.99         7.89        37.05 

$`XQ LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95        12.43         8.48         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 
        6.61       122.73        81.96        75.25        72.92        50.17 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O 
       39.78        37.45        33.57        72.95        24.20        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       27.81        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.61        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 
        1.22        87.45         7.04        11.64        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
       94.52       114.08        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 
      105.21         6.54         8.84       117.40        90.77        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7304 
       10.36         7.96        18.94        62.01        25.91        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         2.76        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       19.13        16.96        15.48        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 
       77.98         7.23        11.41        26.76         7.13       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 
       67.46        41.13        79.99        57.93        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5962 
      130.78        75.02        36.82        32.35         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       25.48        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y 
       23.70        14.76        17.82        16.41        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
       27.52         0.10         6.67        40.11         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       45.99        56.09        57.60        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
       14.96         0.10        17.52         6.90        14.53        39.48 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
        0.10        37.87        33.01         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       28.27         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.14        16.83        21.40        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ 
       19.23         4.31        21.70        21.60        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV 
       12.76        20.81        20.71        42.77        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        6.71         1.64         2.37         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        0.76         0.16        13.25         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU 
       15.16         2.53        12.62        15.85        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        19.86        15.91        18.61        14.07        36.13 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       17.03        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 
       99.06        30.05        98.63        31.59        49.45        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-VM-A8C8 TCGA-VM-A8C9 
       18.61        14.93        23.80        15.98        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS 
       13.51         0.10        35.93        23.47        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.10              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           134.27            211.17 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           16.585            19.035 
[1] "0.1 - 134.3 (16.6)" "0.0 - 211.2 (19.0)"
[1] "hr=" "2"  
D80V2, continuous
D80V3, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    26  39
  XQ LOSS WILD-TYPE 180 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     26   39
  XQ LOSS WILD-TYPE  180  227
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              26               180
  MALE                39               227
[1] 2 2
[1] FALSE
D80V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XQ LOSS MUTATED            24               14                27
  XQ LOSS WILD-TYPE         152              104               151
D80V5, multiclass
                   clus
vv                  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASTROCYTOMA                    24               152
  OLIGOASTROCYTOMA               14               104
  OLIGODENDROGLIOMA              27               151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    13  52
  XQ LOSS WILD-TYPE  79 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13   52
  XQ LOSS WILD-TYPE   79  328
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               13                79
  YES              52               328
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     1
  XQ LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           0    63
  XQ LOSS WILD-TYPE                        15   374
D80V7, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         63               374
[1] 4 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, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3  59
  XQ LOSS WILD-TYPE  15 360
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   59
  XQ LOSS WILD-TYPE   15  360
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              59               360
[1] 2 2
[1] FALSE
