[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/19775312/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/19781938/transformed.cor.cli.txt"

nPatients in clinical file=515, in cluster file=513, common to both=512
[1] "Reduce the number of clustering variables from 82 to 81."
[1]  81 512
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13               499 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13               499 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23               489 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23               489 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               498 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               498 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               499 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               499 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               501 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               501 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               504 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               504 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               499 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               499 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               506 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               506 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               501 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               501 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8               504 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8               504 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               505 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               505 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              121               391 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              121               391 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              151               361 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              151               361 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               46               466 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               46               466 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               56               456 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               56               456 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               495 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               495 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               488 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               488 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                57                455 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                57                455 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                500 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                500 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                481 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                481 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                58                454 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                58                454 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                33                479 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                33                479 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                496 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                496 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                506 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                506 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                508 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                508 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                501 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                501 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                17                495 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                17                495 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                493 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                493 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                492 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                492 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                489 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                489 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                495 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                495 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                499 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                499 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               100                412 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               100                412 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                25                487 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                25                487 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                43                469 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                43                469 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                469 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                469 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                24                488 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                24                488 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                489 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                489 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               21               491 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               21               491 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               39               473 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               39               473 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              184               328 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              184               328 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               487 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               487 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               21               491 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               21               491 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               494 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               494 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               482 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               482 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               28               484 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               28               484 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               71               441 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               71               441 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               92               420 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               92               420 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               478 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               478 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               479 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               479 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               30               482 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               30               482 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               62               450 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               62               450 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               509 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               509 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               509 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               509 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               17               495 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               17               495 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               501 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               501 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              117               395 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              117               395 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50               462 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50               462 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                83                429 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                83                429 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                96                416 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                96                416 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                449 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                449 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                491 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                491 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                26                486 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                26                486 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                51                461 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                51                461 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               116                396 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               116                396 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                80                432 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                80                432 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                51                461 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                51                461 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                498 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                498 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                490 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                490 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                499 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                499 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                504 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                504 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                68                444 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                68                444 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                450 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                450 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                25                487 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                25                487 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               209                303 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               209                303 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                505 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                505 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                509 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                509 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                36                476 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                36                476 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                455 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                455 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               99               413 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               99               413 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               71               441 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               71               441 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "DAYS_TO_LAST_KNOWN_ALIVE"            
 [9] "RADIATION_THERAPY"                   
[10] "KARNOFSKY_PERFORMANCE_SCORE"         
[11] "HISTOLOGICAL_TYPE"                   
[12] "RACE"                                
[13] "ETHNICITY"                           

Input Data has 13 rows and 512 columns.

[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=117,	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=365,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 9:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[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 512 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"              "GENDER"                     
[3] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
[5] "HISTOLOGICAL_TYPE"           "RACE"                       
[7] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, 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   6
  1P GAIN WILD-TYPE 381 115
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13               496 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               115 
$`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        24.43 
TCGA-E1-5304 TCGA-E1-A7YD TCGA-E1-A7YQ TCGA-HT-7686 TCGA-HT-A4DS TCGA-S9-A6WM 
       41.13        14.30        51.88        42.74         0.23        19.86 
TCGA-TM-A84I 
       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        46.95         7.56        49.94        49.12         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 
       91.13        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 
       63.88        46.06         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        23.21        17.46        13.71 
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         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       154.36       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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       29.85        31.69        26.17        24.99        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       21.57        95.11        20.98        22.29        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       17.16        21.30        17.98       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       37.38         7.50        44.42        38.89         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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK 
      130.78        29.13        93.21         3.65        19.46        12.43 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU 
       16.18        21.30        23.90        75.02        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         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 
       52.21        36.82        18.77        14.93        42.54        41.33 
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 
       28.34        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        21.53        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 
       18.64         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-7687 TCGA-HT-7688 TCGA-HT-7689 
        0.76        44.68         6.05         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-A4DV 
        0.23        29.59        34.19        28.27        15.72        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        56.58        13.45        41.49        45.60        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54         6.18 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55        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         7.99         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 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        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-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       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        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.23              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            51.88            211.17 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           19.130            20.995 
[1] "0.2 - 51.9 (19.1)"  "0.0 - 211.2 (21.0)"
[1] "hr=" "3.2"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     8   5
  1P GAIN WILD-TYPE 220 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8    5
  1P GAIN WILD-TYPE  220  279
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               8               220
  MALE                 5               279
[1] 2 2
[1] FALSE
D1V4, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  11
  1P GAIN WILD-TYPE 183 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   11
  1P GAIN WILD-TYPE  183  282
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                1               183
  YES              11               282
[1] 2 2
[1] FALSE
D1V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1P GAIN MUTATED            10                0                 3
  1P GAIN WILD-TYPE         184              129               186
D1V6, multiclass
                   clus
vv                  1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASTROCYTOMA                    10               184
  OLIGOASTROCYTOMA                0               129
  OLIGODENDROGLIOMA               3               186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           1    12
  1P GAIN WILD-TYPE                        20   460
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                      1                20
  WHITE                                         12               460
[1] 4 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  13
  1P GAIN WILD-TYPE  32 433
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   13
  1P GAIN WILD-TYPE   32  433
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO              13               433
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    15   8
  1Q GAIN WILD-TYPE 373 113
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23               486 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8               113 
$`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        24.43        51.52        41.13 
TCGA-E1-A7YD TCGA-E1-A7YQ TCGA-HT-7475 TCGA-HT-7688 TCGA-HT-A4DS TCGA-S9-A6WM 
       14.30        51.88        17.42        31.69         0.23        19.86 
TCGA-TM-A84B TCGA-TM-A84I TCGA-VM-A8CA TCGA-VM-A8CF TCGA-WH-A86K 
       24.92        28.08        13.51        20.02        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        46.95         7.56        49.94        49.12         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 
       91.13        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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       46.06         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        23.21        17.46        13.71        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         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      156.23       154.36       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        33.27        29.85        31.69        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76        17.16        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       84.33        37.38         7.50        44.42        38.89         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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
       95.57       130.78        29.13        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS 
       12.43        16.18        21.30        23.90        75.02        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
        0.76        32.45        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         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        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        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        21.53        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        18.64         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-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-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-A4DV 
        0.23        29.59        34.19        28.27        15.72        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        56.58        13.45        41.49        45.60        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54         6.18 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55        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         7.99         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 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        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-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       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        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       14.93        23.80        21.37        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       40.41        44.09        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       26.14        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       43.04        43.20         0.10         7.89        39.16        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 
           19.860            20.995 
[1] "0.2 - 211.2 (19.9)" "0.0 - 182.3 (21.0)"
[1] "hr=" "1.4"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    12  11
  1Q GAIN WILD-TYPE 216 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     12   11
  1Q GAIN WILD-TYPE  216  273
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              12               216
  MALE                11               273
[1] 2 2
[1] FALSE
D2V4, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     7  15
  1Q GAIN WILD-TYPE 177 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7   15
  1Q GAIN WILD-TYPE  177  278
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                7               177
  YES              15               278
[1] 2 2
[1] FALSE
D2V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1Q GAIN MUTATED            13                2                 8
  1Q GAIN WILD-TYPE         181              127               181
D2V6, multiclass
                   clus
vv                  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASTROCYTOMA                    13               181
  OLIGOASTROCYTOMA                2               127
  OLIGODENDROGLIOMA               8               181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           1    20
  1Q GAIN WILD-TYPE                        20   452
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                      1                20
  WHITE                                         20               452
[1] 4 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  21
  1Q GAIN WILD-TYPE  32 425
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   21
  1Q GAIN WILD-TYPE   32  425
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO              21               425
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED     9   5
  2P GAIN WILD-TYPE 379 116
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               495 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                5               116 
$`2P GAIN MUTATED`
TCGA-DB-5274 TCGA-DH-A669 TCGA-DH-A7UR TCGA-DU-8165 TCGA-E1-5304 TCGA-E1-A7YD 
       75.25        30.21        54.25        19.13        41.13        14.30 
TCGA-E1-A7YV TCGA-HT-8564 TCGA-HT-A4DS TCGA-S9-A6WM TCGA-S9-A7J0 TCGA-TM-A84Q 
       32.45        15.72         0.23        19.86        20.02        25.38 
TCGA-VM-A8CA TCGA-VW-A8FI 
       13.51         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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
       49.12         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        91.13        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        63.88        46.06         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        23.21        17.46        13.71        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         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       154.36        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 
       33.27        29.85        31.69        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76        17.16        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       78.21        95.57       130.78        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       51.88        15.32         0.76        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         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        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        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        21.53 
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        18.64         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-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-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        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        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 
        7.99         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         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       19.20         3.45         2.37         4.41        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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       85.55        38.56        84.99        31.10        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       18.64        14.07        36.13         7.92        26.93        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       19.99         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        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-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       33.24        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        31.36        43.04        43.20         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  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 
            19.94             20.98 
[1] "0.2 - 75.2 (19.9)"  "0.0 - 211.2 (21.0)"
[1] "hr=" "1.9"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     7   7
  2P GAIN WILD-TYPE 221 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      7    7
  2P GAIN WILD-TYPE  221  277
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               7               221
  MALE                 7               277
[1] 2 2
[1] FALSE
D3V4, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     3  10
  2P GAIN WILD-TYPE 181 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   10
  2P GAIN WILD-TYPE  181  283
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                3               181
  YES              10               283
[1] 2 2
[1] FALSE
D3V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2P GAIN MUTATED             7                2                 5
  2P GAIN WILD-TYPE         187              127               184
D3V6, multiclass
                   clus
vv                  2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASTROCYTOMA                     7               187
  OLIGOASTROCYTOMA                2               127
  OLIGODENDROGLIOMA               5               184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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    13
  2P GAIN WILD-TYPE                        21   459
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                21
  WHITE                                         13               459
[1] 4 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  12
  2P GAIN WILD-TYPE  31 434
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1   12
  2P GAIN WILD-TYPE   31  434
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                31
  NOT HISPANIC OR LATINO              12               434
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED     9   4
  2Q GAIN WILD-TYPE 379 117
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               496 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                4               117 
$`2Q GAIN MUTATED`
TCGA-DB-5274 TCGA-DH-A7UR TCGA-DU-8165 TCGA-E1-5304 TCGA-E1-A7YD TCGA-E1-A7YV 
       75.25        54.25        19.13        41.13        14.30        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 

$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
       49.12         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        91.13        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        63.88        46.06         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        23.21        17.46        13.71 
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         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       154.36        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        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
       22.29        11.41        26.76        17.16        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       38.89         0.56        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH 
      134.27        78.21        95.57       130.78        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY 
       75.02        51.88        15.32         0.76        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         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        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        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 
       21.53        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        18.64         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-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       34.19        28.27        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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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        41.10        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
      135.22        85.55        38.56        84.99        31.10        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       23.51        19.99         8.19         2.04        20.68        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       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        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        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-A7RF 
       24.79        33.24        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB 
       61.41        26.99        31.36        43.04        43.20         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        7.89        39.16        20.02        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21        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 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 
           19.860            20.995 
[1] "0.2 - 75.2 (19.9)"  "0.0 - 211.2 (21.0)"
[1] "hr=" "1.7"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     7   6
  2Q GAIN WILD-TYPE 221 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      7    6
  2Q GAIN WILD-TYPE  221  278
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               7               221
  MALE                 6               278
[1] 2 2
[1] FALSE
D4V4, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  10
  2Q GAIN WILD-TYPE 182 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   10
  2Q GAIN WILD-TYPE  182  283
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                2               182
  YES              10               283
[1] 2 2
[1] FALSE
D4V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2Q GAIN MUTATED             7                2                 4
  2Q GAIN WILD-TYPE         187              127               185
D4V6, multiclass
                   clus
vv                  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASTROCYTOMA                     7               187
  OLIGOASTROCYTOMA                2               127
  OLIGODENDROGLIOMA               4               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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    12
  2Q GAIN WILD-TYPE                        21   460
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                21
  WHITE                                         12               460
[1] 4 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  11
  2Q GAIN WILD-TYPE  31 435
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   11
  2Q GAIN WILD-TYPE   31  435
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                31
  NOT HISPANIC OR LATINO              11               435
[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 381 117
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               498 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4               117 
$`3P GAIN MUTATED`
TCGA-CS-6668 TCGA-DU-6400 TCGA-DU-7013 TCGA-DU-8158 TCGA-E1-5304 TCGA-FG-5962 
       49.94         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        46.95         7.56        49.12 
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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        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         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       154.36        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 
       33.27        29.85        31.69        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76        17.16        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       75.02        51.88        15.32         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
      146.14        13.08        73.48       145.05        32.35        39.48 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        25.48        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        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 
       21.53        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        18.64         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-7607 
        5.03        29.85        23.18       122.47         4.57         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-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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        6.71         7.99         2.37         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         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       19.20         3.45         2.37         4.41        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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP 
       85.55        38.56        84.99        31.10        26.47        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        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-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        43.04        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        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 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.23              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            49.94            211.17 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           17.290            21.155 
[1] "0.2 - 49.9 (17.3)"  "0.0 - 211.2 (21.2)"
[1] "hr=" "2.8"
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     6   5
  3P GAIN WILD-TYPE 222 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    5
  3P GAIN WILD-TYPE  222  279
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               6               222
  MALE                 5               279
[1] 2 2
[1] FALSE
D5V4, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3   5
  3P GAIN WILD-TYPE 181 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    5
  3P GAIN WILD-TYPE  181  288
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                3               181
  YES               5               288
[1] 2 2
[1] FALSE
D5V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3P GAIN MUTATED             8                0                 3
  3P GAIN WILD-TYPE         186              129               186
D5V6, multiclass
                   clus
vv                  3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASTROCYTOMA                     8               186
  OLIGOASTROCYTOMA                0               129
  OLIGODENDROGLIOMA               3               186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                        21   461
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                21
  WHITE                                         11               461
[1] 4 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  32 435
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   11
  3P GAIN WILD-TYPE   32  435
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO              11               435
[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 384 117
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               501 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4               117 
$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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 
        2.40        11.47        62.96       156.23       154.36        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        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
       22.29        11.41        26.76        17.16        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       38.89         0.56        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE 
      134.27        78.21        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
       93.21         3.65        19.46        12.43        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       23.90        75.02        51.88        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       39.48         0.23         0.20        25.48        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        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        28.34        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        21.53        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        18.64         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        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       26.93        23.51        19.99        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       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 
       20.48        54.77        48.33        49.32        34.78        65.39 
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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       14.93        23.80        21.37        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       40.41        44.09        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       26.14        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        43.20        13.51         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        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 

  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            21.010 
[1] "0.2 - 47.8 (13.1)"  "0.0 - 211.2 (21.0)"
[1] "hr=" "4.3"
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5   3
  3Q GAIN WILD-TYPE 223 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5    3
  3Q GAIN WILD-TYPE  223  281
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               5               223
  MALE                 3               281
[1] 2 2
[1] FALSE
D6V4, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     1   5
  3Q GAIN WILD-TYPE 183 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1    5
  3Q GAIN WILD-TYPE  183  288
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                1               183
  YES               5               288
[1] 2 2
[1] FALSE
D6V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3Q GAIN MUTATED             6                0                 2
  3Q GAIN WILD-TYPE         188              129               187
D6V6, multiclass
                   clus
vv                  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASTROCYTOMA                     6               188
  OLIGOASTROCYTOMA                0               129
  OLIGODENDROGLIOMA               2               187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                        21   464
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                21
  WHITE                                          8               464
[1] 4 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  32 438
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0    8
  3Q GAIN WILD-TYPE   32  438
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               8               438
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    11   2
  4P GAIN WILD-TYPE 377 119
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               496 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               119 
$`4P GAIN MUTATED`
TCGA-CS-4943 TCGA-CS-6665 TCGA-CS-6666 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-E1-A7YD 
       18.15        12.43        46.95        31.69        24.43        14.30 
TCGA-E1-A7YQ TCGA-FG-A87Q TCGA-HT-7477 TCGA-HT-7857 TCGA-HT-A5R7 TCGA-S9-A6TU 
       51.88         5.72        24.26         0.23        20.22        87.12 
TCGA-S9-A7J0 
       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        49.94        49.12         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        91.13 
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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       46.06         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        23.21        17.46        13.71        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         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       154.36        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        33.27        29.85        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76        17.16        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       78.21        95.57       130.78        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       15.32         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         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        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        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        21.53 
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-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       48.69        20.45        18.64        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-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-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-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        56.58        13.45        41.49        45.60        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54         6.18 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55        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         7.99         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 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        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-A6TV 
       28.08         2.07        19.59        30.67        62.17        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       41.10        28.14        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 
       36.13         7.92        26.93        23.51        19.99         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
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        20.48        54.77        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  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 
           20.220            20.895 
[1] "0.2 - 87.1 (20.2)"  "0.0 - 211.2 (20.9)"
[1] "hr=" "1.3"
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6   7
  4P GAIN WILD-TYPE 222 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    7
  4P GAIN WILD-TYPE  222  277
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6               222
  MALE                 7               277
[1] 2 2
[1] FALSE
D7V4, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3  10
  4P GAIN WILD-TYPE 181 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   10
  4P GAIN WILD-TYPE  181  283
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                3               181
  YES              10               283
[1] 2 2
[1] FALSE
D7V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4P GAIN MUTATED             9                0                 4
  4P GAIN WILD-TYPE         185              129               185
D7V6, multiclass
                   clus
vv                  4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASTROCYTOMA                     9               185
  OLIGOASTROCYTOMA                0               129
  OLIGODENDROGLIOMA               4               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           2    11
  4P GAIN WILD-TYPE                        19   461
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                      2                19
  WHITE                                         11               461
[1] 4 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  12
  4P GAIN WILD-TYPE  32 434
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   12
  4P GAIN WILD-TYPE   32  434
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO              12               434
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     4   2
  4Q GAIN WILD-TYPE 384 119
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               503 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               119 
$`4Q GAIN MUTATED`
TCGA-DU-A5TT TCGA-E1-A7YD TCGA-HT-7477 TCGA-HT-7857 TCGA-HT-A5R7 TCGA-VW-A8FI 
       24.43        14.30        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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       31.69        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       95.11        20.98        22.29        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
        7.50        44.42        38.89         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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK 
      130.78        29.13        93.21         3.65        19.46        12.43 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS 
       16.18        21.30        23.90        75.02        51.88        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
        0.76        32.45        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         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        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        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        21.53        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        18.64         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-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-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-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        56.58        13.45        41.49        45.60        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54         6.18 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55        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         7.99         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 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        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-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        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-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        43.04        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        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 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.23              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            24.43            211.17 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            17.26             20.98 
[1] "0.2 - 24.4 (17.3)"  "0.0 - 211.2 (21.0)"
[1] "hr=" "3.5"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     2   4
  4Q GAIN WILD-TYPE 226 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    4
  4Q GAIN WILD-TYPE  226  280
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2               226
  MALE                 4               280
[1] 2 2
[1] FALSE
D8V4, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   5
  4Q GAIN WILD-TYPE 183 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    5
  4Q GAIN WILD-TYPE  183  288
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1               183
  YES               5               288
[1] 2 2
[1] FALSE
D8V5, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               304 
       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-6401        TCGA-DU-6403 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-6404        TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-6410        TCGA-DU-7009        TCGA-DU-7011        TCGA-DU-7013 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299        TCGA-DU-7300 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304        TCGA-DU-7306 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161        TCGA-DU-8162 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-8163        TCGA-DU-8165        TCGA-DU-8167        TCGA-DU-8168 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A6S2        TCGA-DU-A6S6        TCGA-DU-A6S7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A6S8        TCGA-DU-A76R        TCGA-DU-A7T6        TCGA-DU-A7T8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A7TA        TCGA-DU-A7TB        TCGA-DU-A7TC        TCGA-DU-A7TD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A7TG        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-E1-A7YE        TCGA-E1-A7YH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-A7YI        TCGA-E1-A7YJ        TCGA-E1-A7YK        TCGA-E1-A7YL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-A7YM        TCGA-E1-A7YN        TCGA-E1-A7YO        TCGA-E1-A7YQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-A7YS        TCGA-E1-A7YV        TCGA-E1-A7YW        TCGA-E1-A7YY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-A7Z2        TCGA-E1-A7Z4        TCGA-E1-A7Z6        TCGA-FG-5963 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-8181 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-A4MT        TCGA-FG-A4MW        TCGA-FG-A4MX 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-A60J        TCGA-FG-A60L        TCGA-FG-A6J1        TCGA-FG-A6J3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-A711        TCGA-FG-A713        TCGA-FG-A87Q        TCGA-HT-7468 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7470        TCGA-HT-7475        TCGA-HT-7481        TCGA-HT-7482 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7485        TCGA-HT-7607        TCGA-HT-7609        TCGA-HT-7611 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7686        TCGA-HT-7689        TCGA-HT-7692        TCGA-HT-7693 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7694        TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7858        TCGA-HT-7875        TCGA-HT-7884        TCGA-HT-8013 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-8105        TCGA-HT-8113        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-A7RG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TQ-A7RK        TCGA-TQ-A7RM        TCGA-TQ-A7RN        TCGA-TQ-A7RO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TQ-A7RP        TCGA-TQ-A7RQ        TCGA-TQ-A7RR        TCGA-TQ-A7RS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TQ-A7RU        TCGA-TQ-A7RV        TCGA-TQ-A7RW        TCGA-TQ-A8XE 
"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-A8CF        TCGA-VM-A8CH        TCGA-WY-A858        TCGA-WY-A859 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4Q GAIN MUTATED             5                0                 1
  4Q GAIN WILD-TYPE         189              129               188
D8V6, multiclass
                   clus
vv                  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASTROCYTOMA                     5               189
  OLIGOASTROCYTOMA                0               129
  OLIGODENDROGLIOMA               1               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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     6
  4Q GAIN WILD-TYPE                        21   466
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                21
  WHITE                                          6               466
[1] 4 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   6
  4Q GAIN WILD-TYPE  32 440
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    6
  4Q GAIN WILD-TYPE   32  440
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               6               440
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED     5   6
  5P GAIN WILD-TYPE 383 115
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               498 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6               115 
$`5P GAIN MUTATED`
TCGA-DU-A5TT TCGA-E1-5304 TCGA-E1-A7YD TCGA-E1-A7YQ TCGA-HT-7477 TCGA-QH-A65S 
       24.43        41.13        14.30        51.88        24.26         2.53 
TCGA-QH-A6CV TCGA-S9-A6TS TCGA-TM-A7C3 TCGA-VM-A8C9 TCGA-VW-A8FI 
       14.53        62.17        54.77        43.20         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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       31.69        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       95.11        20.98        22.29        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
        7.50        44.42        38.89         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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       29.13        93.21         3.65        19.46        12.43        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       21.30        23.90        75.02        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       39.48         0.23         0.20        47.77        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        42.54        41.33        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        28.34 
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        21.53        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        18.64 
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-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        56.58        13.45        41.49        45.60        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54         6.18 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55        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         7.99         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 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        2.37         4.41        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        41.10        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       26.93        23.51        19.99        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       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-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       20.48        48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       25.87        33.93        61.41        26.99        31.36        43.04 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        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 

  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 
            24.43             20.76 
[1] "2.5 - 62.2 (24.4)"  "0.0 - 211.2 (20.8)"
[1] "hr=" "2.4"
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     5   6
  5P GAIN WILD-TYPE 223 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5    6
  5P GAIN WILD-TYPE  223  278
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               5               223
  MALE                 6               278
[1] 2 2
[1] FALSE
D9V4, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3   8
  5P GAIN WILD-TYPE 181 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3    8
  5P GAIN WILD-TYPE  181  285
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                3               181
  YES               8               285
[1] 2 2
[1] FALSE
D9V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5P GAIN MUTATED             7                2                 2
  5P GAIN WILD-TYPE         187              127               187
D9V6, multiclass
                   clus
vv                  5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASTROCYTOMA                     7               187
  OLIGOASTROCYTOMA                2               127
  OLIGODENDROGLIOMA               2               187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           1     8
  5P GAIN WILD-TYPE                        20   464
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                      1                20
  WHITE                                          8               464
[1] 4 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  10
  5P GAIN WILD-TYPE  32 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0   10
  5P GAIN WILD-TYPE   32  436
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO              10               436
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     4   4
  5Q GAIN WILD-TYPE 384 117
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8               501 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4               117 
$`5Q GAIN MUTATED`
TCGA-DU-A5TT TCGA-E1-A7YD TCGA-E1-A7YQ TCGA-QH-A65S TCGA-QH-A6CV TCGA-TM-A7C3 
       24.43        14.30        51.88         2.53        14.53        54.77 
TCGA-VM-A8C9 TCGA-VW-A8FI 
       43.20         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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       31.69        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       95.11        20.98        22.29        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
        7.50        44.42        38.89         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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK 
      130.78        29.13        93.21         3.65        19.46        12.43 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU 
       16.18        21.30        23.90        75.02        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         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 
       52.21        36.82        18.77        14.93        42.54        41.33 
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 
       28.34        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        21.53        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 
       18.64         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-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        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        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 
        7.99         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         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V 
       19.20         3.45         2.37         4.41        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-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        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        31.59        18.71        20.48        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        31.36        43.04        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2.53              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            54.77            211.17 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            19.48             20.81 
[1] "2.5 - 54.8 (19.5)"  "0.0 - 211.2 (20.8)"
[1] "hr=" "2.6"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     4   4
  5Q GAIN WILD-TYPE 224 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    4
  5Q GAIN WILD-TYPE  224  280
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               4               224
  MALE                 4               280
[1] 2 2
[1] FALSE
D10V4, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3   5
  5Q GAIN WILD-TYPE 181 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    5
  5Q GAIN WILD-TYPE  181  288
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                3               181
  YES               5               288
[1] 2 2
[1] FALSE
D10V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5Q GAIN MUTATED             4                2                 2
  5Q GAIN WILD-TYPE         190              127               187
D10V6, multiclass
                   clus
vv                  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASTROCYTOMA                     4               190
  OLIGOASTROCYTOMA                2               127
  OLIGODENDROGLIOMA               2               187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           1     5
  5Q GAIN WILD-TYPE                        20   467
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                      1                20
  WHITE                                          5               467
[1] 4 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   7
  5Q GAIN WILD-TYPE  32 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    7
  5Q GAIN WILD-TYPE   32  439
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               7               439
[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 382 120
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               502 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1               120 
$`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         2.40        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        46.95         7.56        49.94        49.12 
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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        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       154.36        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        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
       22.29        11.41        26.76        17.16        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       38.89         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-A7YD 
       57.93       134.27        78.21        95.57       130.78        14.30 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       29.13        93.21         3.65        19.46        12.43        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU 
       21.30        23.90        75.02        51.88        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         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 
       52.21        36.82        18.77        14.93        42.54        41.33 
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 
       28.34        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        21.53        15.02        16.44 
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        18.64 
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-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        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 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
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        20.48        54.77        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  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 
           17.290            20.895 
[1] "2.3 - 114.1 (17.3)" "0.0 - 211.2 (20.9)"
[1] "hr=" "1.5"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5   2
  6P GAIN WILD-TYPE 223 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    2
  6P GAIN WILD-TYPE  223  282
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5               223
  MALE                 2               282
[1] 2 2
[1] FALSE
D11V4, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0   6
  6P GAIN WILD-TYPE 184 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    6
  6P GAIN WILD-TYPE  184  287
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                0               184
  YES               6               287
[1] 2 2
[1] FALSE
D11V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6P GAIN MUTATED             5                1                 1
  6P GAIN WILD-TYPE         189              128               188
D11V6, multiclass
                   clus
vv                  6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASTROCYTOMA                     5               189
  OLIGOASTROCYTOMA                1               128
  OLIGODENDROGLIOMA               1               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                        21   465
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                21
  WHITE                                          7               465
[1] 4 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  32 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    7
  6P GAIN WILD-TYPE   32  439
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               7               439
[1] 2 2
[1] FALSE

Clustering(12) Variable = 7P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    72  49
  7P GAIN WILD-TYPE 316  72
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              121               388 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               49                72 
$`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        17.46 
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        29.85        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R 
       26.17        24.99        33.96        11.41        26.76        21.30 
TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YD 
       84.33         7.50         0.56        41.13       130.78        14.30 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YQ TCGA-E1-A7Z2 
       19.46        16.18        21.30        23.90        51.88        13.08 
TCGA-FG-5962 TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 
       47.77        18.77        41.33        18.44        15.35        20.09 
TCGA-FG-8182 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7473 
       13.68        10.72        18.38        10.78         5.72        16.54 
TCGA-HT-7477 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8011 TCGA-HT-8013 
       24.26         0.49         3.72        11.28        16.24        63.55 
TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 
       12.23        13.78        15.72         0.23         0.13         0.07 
TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
        5.33        16.14        21.40        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-P5-A72U TCGA-P5-A731 TCGA-P5-A736 
       15.35        14.40         4.11         0.23         9.01         7.56 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-RY-A845 TCGA-S9-A6TY 
       19.33        14.53         1.91         5.03        19.59        35.38 
TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 
       24.39        19.86        36.13        26.93        19.99        20.02 
TCGA-S9-A7QW TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H 
       15.06        10.39        54.77        34.78        24.92        30.44 
TCGA-TM-A84M TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RM TCGA-TQ-A7RP TCGA-VW-A8FI 
       24.79        15.98         2.04        36.69        30.05         8.05 
TCGA-WY-A85E 
       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        46.95         7.56        49.94        49.12        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        91.13        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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR 
       46.06         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 
       23.21        13.71        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         2.40        62.96       156.23       154.36        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 
       33.27        31.69        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC 
       22.29        17.16        17.98       139.04        51.52        37.38 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       44.42        38.89        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
      134.27        78.21        95.57        29.13        93.21         3.65 
TCGA-E1-A7YK TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       12.43        75.02        15.32         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      146.14        73.48       145.05        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
        0.20        25.48        52.21        36.82        14.93        42.54 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8186 
       17.88        22.55        20.61        28.34        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX 
       20.09        14.96        22.52        32.61        38.27        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        21.53        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       22.26        28.54        36.66        48.69        20.45        18.64 
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-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
        0.03         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-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-7902 TCGA-HT-8010 TCGA-HT-8012 
        3.68         5.33        35.47        31.43         1.64         9.40 
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-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-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 
       26.04        20.22        27.35         0.10         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        1.81        16.83        17.52        11.05         0.10        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        12.76 
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-A5F1 TCGA-P5-A5F2 
        6.71         7.99         2.37         2.30         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        10.95 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
       13.61         9.60        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        15.16         2.53        12.62        15.85        14.04 
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-A6XA TCGA-QH-A86X TCGA-QH-A870 
       14.53        16.34        16.73        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-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
        9.90        28.08         2.07        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 
       18.77        41.10        28.14        36.82        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IY 
       26.47        18.61        18.64        14.07         7.92        23.51 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        8.19         2.04        20.68        18.54        28.37        27.16 
TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
      169.84        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       20.48        48.33        49.32        65.39        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q 
       40.64        28.08        24.16        40.83        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RJ 
       18.61        14.93        23.80        21.37        19.69        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       44.09        33.73        31.20        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        43.04        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        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 
       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 
            18.44             23.21 
[1] "0.1 - 211.2 (18.4)" "0.0 - 182.3 (23.2)"
[1] "hr=" "2.8"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    60  61
  7P GAIN WILD-TYPE 168 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     60   61
  7P GAIN WILD-TYPE  168  223
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              60               168
  MALE                61               223
[1] 2 2
[1] FALSE
D12V4, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    28  84
  7P GAIN WILD-TYPE 156 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     28   84
  7P GAIN WILD-TYPE  156  209
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               28               156
  YES              84               209
[1] 2 2
[1] FALSE
D12V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7P GAIN MUTATED            53               31                37
  7P GAIN WILD-TYPE         141               98               152
D12V6, multiclass
                   clus
vv                  7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASTROCYTOMA                    53               141
  OLIGOASTROCYTOMA               31                98
  OLIGODENDROGLIOMA              37               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"
                   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                          10   108
  7P GAIN WILD-TYPE                        11   364
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                     10                11
  WHITE                                        108               364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     8 108
  7P GAIN WILD-TYPE  24 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8  108
  7P GAIN WILD-TYPE   24  338
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                24
  NOT HISPANIC OR LATINO             108               338
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    95  56
  7Q GAIN WILD-TYPE 293  65
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              151               358 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               56                65 
$`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        17.46        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        29.85        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L 
       26.17        24.99        33.96        95.11        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5302 
       21.30       139.04        84.33         7.50         0.56        50.14 
TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM 
       41.13       130.78        14.30        19.46        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YQ TCGA-E1-A7Z3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5965 
       23.90        51.88        73.48         0.20        47.77        36.82 
TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 
       18.77        42.54        41.33        18.44        15.35        20.09 
TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q 
       13.68        16.01        10.72        18.38        10.78         5.72 
TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7610 TCGA-HT-7693 
       16.54        17.42        24.26       122.47        56.09        17.52 
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-8108 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 
        2.50        13.78        15.72         0.23         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61C 
       27.35         5.33         1.81        16.14        21.40        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7495 TCGA-HW-8322 
        2.43        10.52        15.35         0.10        35.44         6.18 
TCGA-HW-A5KJ TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A72U 
       10.55        14.40         0.23         2.30         4.11         0.23 
TCGA-P5-A731 TCGA-P5-A736 TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX 
        9.01         7.56        19.33        14.83        14.53        12.23 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-RY-A845 TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM 
       16.50         5.03        19.59        35.38        24.39        19.86 
TCGA-S9-A6WO TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW 
       18.61        36.13        26.93        19.99        20.02        15.06 
TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A84B 
       28.37        10.39        54.77        48.33        34.78        24.92 
TCGA-TM-A84H TCGA-TM-A84M TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RP TCGA-VW-A8FI 
       30.44        24.79        15.98         2.04        30.05         8.05 
TCGA-WY-A85E 
       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        46.95         7.56        49.94        49.12        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        91.13        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        63.88        46.06         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        23.21        13.71 
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         2.40        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
      154.36        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 
       33.27        31.69        25.55        21.57        20.98        22.29 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI 
       17.16        17.98        51.52        37.38        44.42        38.89 
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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YO TCGA-E1-A7YS 
       29.13        93.21         3.65        12.43        75.02        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z4 
        0.76        32.45        36.82       146.14        13.08       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 
       32.35        39.48         0.23        25.48        52.21        14.93 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8187 
       17.88        22.55        20.61        28.34        14.24        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        21.53        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 
       28.54        36.66        48.69        20.45        18.64        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-7474 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        3.75         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-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 
        4.57        17.29         3.16        22.06        45.99        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-7902 TCGA-HT-8010 
        0.13         3.68         5.33        35.47        31.43         1.64 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
        9.40         0.10        37.87        33.01         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        0.46         5.56         0.23        29.59        34.19        28.27 
TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A618 
       26.04        20.22         0.10         2.70        16.93        16.83 
TCGA-HT-A61B TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       17.52        11.05        56.58        13.45        41.49        45.60 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK 
       68.32        69.27        39.75        40.01        42.54        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EW 
       20.81        20.71        19.00        42.77        14.40         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        7.99         2.37         5.88         7.63         0.76         1.28 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A733 TCGA-P5-A735 
       10.42        13.25        11.64        10.95        13.61         9.60 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CW TCGA-QH-A6CY 
        2.53        12.62        15.85        14.04        13.61         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-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        41.10        28.14        36.82 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS 
       84.99        31.10        26.47        18.64        14.07         7.92 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QZ 
       23.51         8.19         2.04        20.68        18.54        27.16 
TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
      169.84        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       20.48        49.32        65.39        16.18        59.05        40.64 
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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       14.93        23.80        21.37        19.69        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       36.69        33.73        31.20        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        43.04        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        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 
       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 
            18.51             23.26 
[1] "0.1 - 211.2 (18.5)" "0.0 - 182.3 (23.3)"
[1] "hr=" "2.5"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    71  80
  7Q GAIN WILD-TYPE 157 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     71   80
  7Q GAIN WILD-TYPE  157  204
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              71               157
  MALE                80               204
[1] 2 2
[1] FALSE
D13V4, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    37 101
  7Q GAIN WILD-TYPE 147 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     37  101
  7Q GAIN WILD-TYPE  147  192
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               37               147
  YES             101               192
[1] 2 2
[1] FALSE
D13V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7Q GAIN MUTATED            68               39                44
  7Q GAIN WILD-TYPE         126               90               145
D13V6, multiclass
                   clus
vv                  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASTROCYTOMA                    68               126
  OLIGOASTROCYTOMA               39                90
  OLIGODENDROGLIOMA              44               145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                          12   135
  7Q GAIN WILD-TYPE                         9   337
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                     12                 9
  WHITE                                        135               337
[1] 4 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     8 138
  7Q GAIN WILD-TYPE  24 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8  138
  7Q GAIN WILD-TYPE   24  308
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                24
  NOT HISPANIC OR LATINO             138               308
[1] 2 2
[1] FALSE

Clustering(14) Variable = 8P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    36  10
  8P GAIN WILD-TYPE 352 111
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               46               463 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10               111 
$`8P GAIN MUTATED`
TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5281 TCGA-DB-A64X TCGA-DH-A669 TCGA-DH-A7UT 
       12.43        46.95        78.28        18.51        30.21        17.46 
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        31.69        20.98        17.98        84.33        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        35.38        38.56        18.61        18.54 
TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84Q TCGA-TQ-A7RH TCGA-TQ-A7RQ 
       20.48        65.39        30.44        25.38        15.98        26.14 
TCGA-TQ-A7RV TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-VM-A8CF 
       61.41        43.04        13.51        20.02 

$`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        49.94        49.12         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 
       91.13        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        63.88        46.06 
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 
       23.21        13.71        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         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       154.36        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        33.27        29.85        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       26.17        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
       22.29        11.41        26.76        17.16        21.30       139.04 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         0.56 
TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       95.57       130.78        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       51.88        15.32         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        25.48        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       42.54        41.33        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        28.34        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       14.96        22.52        32.61        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        21.53        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 
       18.64         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-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        6.38        75.19        95.93       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-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-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        1.64         9.40         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-8113 
        6.25         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-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-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        2.43        15.35        11.05         0.10        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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        41.10        28.14 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP 
       85.55        84.99        31.10        19.86        26.47        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY 
       20.02         8.19         2.04        20.68        15.06        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       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        54.77        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       21.37        19.69         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RW 
       33.73        31.20        30.05        25.87        33.93        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       31.36        43.20         0.10         7.89        39.16        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 
           22.145            20.810 
[1] "0.1 - 117.4 (22.1)" "0.0 - 211.2 (20.8)"
[1] "hr=" "1.2"
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    18  28
  8P GAIN WILD-TYPE 210 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     18   28
  8P GAIN WILD-TYPE  210  256
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              18               210
  MALE                28               256
[1] 2 2
[1] FALSE
D14V4, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    11  33
  8P GAIN WILD-TYPE 173 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     11   33
  8P GAIN WILD-TYPE  173  260
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               11               173
  YES              33               260
[1] 2 2
[1] FALSE
D14V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8P GAIN MUTATED            22               11                13
  8P GAIN WILD-TYPE         172              118               176
D14V6, multiclass
                   clus
vv                  8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASTROCYTOMA                    22               172
  OLIGOASTROCYTOMA               11               118
  OLIGODENDROGLIOMA              13               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"
                   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                           2    43
  8P GAIN WILD-TYPE                        19   429
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                      2                19
  WHITE                                         43               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"
D14V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     4  39
  8P GAIN WILD-TYPE  28 407
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4   39
  8P GAIN WILD-TYPE   28  407
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                28
  NOT HISPANIC OR LATINO              39               407
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    43  13
  8Q GAIN WILD-TYPE 345 108
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               56               453 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               13               108 
$`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        46.95        50.86        78.28        18.51 
TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A7UT TCGA-DU-5871 TCGA-DU-6407 TCGA-DU-7013 
       46.06        30.21        17.46        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        31.69        24.99 
TCGA-DU-A6S7 TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-E1-5303 TCGA-E1-A7YY TCGA-FG-5962 
       20.98        17.98        84.33        67.46       146.14        47.77 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-A4MT TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 
       41.33        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-P5-A5F1 TCGA-S9-A6TY TCGA-S9-A6WH TCGA-S9-A6WO 
       20.22        10.52         5.88        35.38        38.56        18.61 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84Q 
       15.06        18.54        20.48        65.39        30.44        25.38 
TCGA-TQ-A7RH TCGA-TQ-A7RM TCGA-TQ-A7RQ TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-VM-A8C8 
       15.98        36.69        26.14        61.41        26.99        43.04 
TCGA-VM-A8CA TCGA-VM-A8CF 
       13.51        20.02 

$`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        49.94        49.12         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        91.13        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        63.88         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        23.21        13.71        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         2.40        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7015 TCGA-DU-7018 
      154.36        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 
       33.27        29.85        24.43        26.17        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       21.57        95.11        22.29        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
       21.30       139.04        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       38.89         0.56        50.14        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE 
      134.27        78.21        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
       93.21         3.65        19.46        12.43        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       23.90        75.02        51.88        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
       36.82        13.08        73.48       145.05        32.35        39.48 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        25.48        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       14.93        42.54        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        28.34        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       14.96        22.52        32.61        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        21.53        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 
       18.64         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-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        6.38        75.19        95.93       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-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-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        1.64         9.40         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-8113 
        6.25         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-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-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        2.43        15.35        11.05         0.10        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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-A5F2 
        6.71         7.99         2.37         2.30         4.11         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       19.20         3.45         2.37         4.41        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-A6TZ 
       62.17        87.12        18.77        41.10        28.14        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       24.39        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       123.65        75.25       135.22        85.55 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        19.86        26.47        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.19         2.04        20.68        28.37        27.16       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-A84B TCGA-TM-A84C 
       54.77        48.33        49.32        34.78        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-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       33.24        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
        2.04        40.41        44.09        33.73        31.20        30.05 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
       25.87        33.93        31.36        43.20         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       39.16        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 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           146.14            211.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           24.625            20.680 
[1] "0.1 - 146.1 (24.6)" "0.0 - 211.2 (20.7)"
[1] "hr=" "1.2"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    23  33
  8Q GAIN WILD-TYPE 205 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     23   33
  8Q GAIN WILD-TYPE  205  251
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              23               205
  MALE                33               251
[1] 2 2
[1] FALSE
D15V4, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    13  40
  8Q GAIN WILD-TYPE 171 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     13   40
  8Q GAIN WILD-TYPE  171  253
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               13               171
  YES              40               253
[1] 2 2
[1] FALSE
D15V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8Q GAIN MUTATED            28               13                15
  8Q GAIN WILD-TYPE         166              116               174
D15V6, multiclass
                   clus
vv                  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASTROCYTOMA                    28               166
  OLIGOASTROCYTOMA               13               116
  OLIGODENDROGLIOMA              15               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"
                   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                           3    51
  8Q GAIN WILD-TYPE                        18   421
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                      3                18
  WHITE                                         51               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"
D15V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     6  46
  8Q GAIN WILD-TYPE  26 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6   46
  8Q GAIN WILD-TYPE   26  400
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                26
  NOT HISPANIC OR LATINO              46               400
[1] 2 2
[1] FALSE

Clustering(16) Variable = 9P GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    12   5
  9P GAIN WILD-TYPE 376 116
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               492 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                5               116 
$`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-E1-A7Z3 TCGA-HT-7474 
       19.13        24.43        17.16        50.14        73.48         3.75 
TCGA-HT-A61B TCGA-S9-A6WH TCGA-S9-A6WM TCGA-TM-A7C4 TCGA-TQ-A7RM 
       17.52        38.56        19.86        48.33        36.69 

$`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        46.95         7.56        49.94        49.12         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 
       91.13        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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       46.06         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        23.21        17.46        13.71        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         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       154.36       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        33.27        29.85        31.69 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       26.17        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 
       20.98        22.29        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 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       38.89         0.56        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE 
      134.27        78.21        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
       93.21         3.65        19.46        12.43        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       23.90        75.02        51.88        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
       36.82       146.14        13.08       145.05        32.35        39.48 
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        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        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        28.34        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        21.53        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        18.64         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-7477 TCGA-HT-7478 
        0.03        16.54        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-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        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       75.25       135.22        85.55        84.99        31.10        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        18.54        28.37        27.16       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        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       54.77        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        43.04        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        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 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             3.75              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            73.48            211.17 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           19.860            20.895 
[1] "3.8 - 73.5 (19.9)"  "0.0 - 211.2 (20.9)"
[1] "hr=" "1.6"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    12   5
  9P GAIN WILD-TYPE 216 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     12    5
  9P GAIN WILD-TYPE  216  279
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              12               216
  MALE                 5               279
[1] 2 2
[1] FALSE
D16V4, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  14
  9P GAIN WILD-TYPE 182 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   14
  9P GAIN WILD-TYPE  182  279
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2               182
  YES              14               279
[1] 2 2
[1] FALSE
D16V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9P GAIN MUTATED             9                5                 3
  9P GAIN WILD-TYPE         185              124               186
D16V6, multiclass
                   clus
vv                  9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASTROCYTOMA                     9               185
  OLIGOASTROCYTOMA                5               124
  OLIGODENDROGLIOMA               3               186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           1    16
  9P GAIN WILD-TYPE                        20   456
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                      1                20
  WHITE                                         16               456
[1] 4 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     1  16
  9P GAIN WILD-TYPE  31 430
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   16
  9P GAIN WILD-TYPE   31  430
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                31
  NOT HISPANIC OR LATINO              16               430
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9Q GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    17   7
  9Q GAIN WILD-TYPE 371 114
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               485 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               114 
$`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-E1-A7Z3 
       23.74        19.13        24.43        17.16        50.14        73.48 
TCGA-FG-A4MY TCGA-FG-A6J3 TCGA-FG-A87N TCGA-HT-7477 TCGA-HT-A61B TCGA-HW-8319 
       23.70        22.26        18.64        24.26        17.52        39.75 
TCGA-S9-A6TW TCGA-S9-A6WH TCGA-S9-A6WM TCGA-S9-A7QW TCGA-TQ-A7RM TCGA-WY-A85E 
       41.10        38.56        19.86        15.06        36.69        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        46.95         7.56        49.94        49.12         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 
       91.13        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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       46.06         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        23.21        17.46        13.71        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         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       154.36       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        33.27        29.85        31.69        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       22.29        11.41        26.76        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       75.02        51.88        15.32         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      146.14        13.08       145.05        32.35        39.48         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        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        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-A60J TCGA-FG-A60K TCGA-FG-A60L 
       10.72        18.38        18.71        14.76        17.82        21.53 
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-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-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         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        56.58        13.45        41.49        45.60        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       69.27        35.44        40.01        42.54         6.18        10.55 
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         7.99         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         0.23 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        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-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       75.25       135.22        85.55        84.99        31.10        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       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        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        43.04        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        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 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             5.10              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            73.48            211.17 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           21.535            20.810 
[1] "5.1 - 73.5 (21.5)"  "0.0 - 211.2 (20.8)"
[1] "hr=" "1.7"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    18   6
  9Q GAIN WILD-TYPE 210 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     18    6
  9Q GAIN WILD-TYPE  210  278
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              18               210
  MALE                 6               278
[1] 2 2
[1] FALSE
D17V4, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  21
  9Q GAIN WILD-TYPE 182 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   21
  9Q GAIN WILD-TYPE  182  272
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                2               182
  YES              21               272
[1] 2 2
[1] FALSE
D17V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9Q GAIN MUTATED            14                6                 4
  9Q GAIN WILD-TYPE         180              123               185
D17V6, multiclass
                   clus
vv                  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASTROCYTOMA                    14               180
  OLIGOASTROCYTOMA                6               123
  OLIGODENDROGLIOMA               4               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           2    21
  9Q GAIN WILD-TYPE                        19   451
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                      2                19
  WHITE                                         21               451
[1] 4 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     2  21
  9Q GAIN WILD-TYPE  30 425
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   21
  9Q GAIN WILD-TYPE   30  425
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                30
  NOT HISPANIC OR LATINO              21               425
[1] 2 2
[1] FALSE

Clustering(18) Variable = 10P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    44  13
  10P GAIN WILD-TYPE 344 108
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                57                452 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                13                108 
$`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 
       13.71        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-A7YI 
       23.31        29.85        31.69        41.13       130.78         3.65 
TCGA-E1-A7YK TCGA-E1-A7YW TCGA-FG-A4MY TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A87N 
       12.43        36.82        23.70        21.53        28.54        18.64 
TCGA-HT-7470 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 
       40.11        16.54         6.54        40.34       106.95       172.77 
TCGA-HT-7688 TCGA-HT-7879 TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-A74O 
       31.69         3.68         0.10         0.23        34.19         0.10 
TCGA-HW-7493 TCGA-IK-7675 TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72X TCGA-P5-A780 
       69.27        19.00         2.30         5.88        13.25         2.37 
TCGA-QH-A6XA TCGA-RY-A83Z TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A89Z TCGA-TM-A7CA 
       16.50         9.90         7.92        20.02        20.48        34.78 
TCGA-TM-A84H TCGA-TQ-A7RH TCGA-TQ-A7RV TCGA-VM-A8C8 TCGA-WH-A86K TCGA-WY-A858 
       30.44        15.98        61.41        43.04        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85E 
       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        46.95        49.94        49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       17.46        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         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       154.36        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        33.27        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
       22.29        11.41        26.76        17.16        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       38.89         0.56        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
      134.27        78.21        95.57        14.30        29.13        93.21 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ 
       19.46        16.18        21.30        23.90        75.02        51.88 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       15.32         0.76        32.45       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         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        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        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-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       18.71        14.76        17.82        15.02        16.44        22.26 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 
       10.78        36.66        48.69        20.45         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 
        0.10         6.67        11.54         0.13         0.03         3.75 
TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7485 
       17.42        24.26         6.38        75.19        95.93         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-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        0.13         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-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-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       13.78        29.59        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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       56.58        13.45        41.49        45.60        68.32        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 
        6.71         7.99         2.37         4.11         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        1.28         0.23        10.42        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        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-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-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        41.10        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX 
       26.47        18.61        18.64        14.07        36.13        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       23.51        19.99         8.19         2.04        20.68        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       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        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        65.39        24.92        16.18        59.05        40.64 
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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI 
       18.61        14.93        23.80        21.37        19.69         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       40.41        44.09        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 
       26.14        25.87        33.93        26.99        31.36        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A85B 
       37.05        16.01        23.21         8.05        51.06        45.80 
TCGA-WY-A85C TCGA-WY-A85D 
       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 
            23.310             20.695 
[1] "0.1 - 172.8 (23.3)" "0.0 - 211.2 (20.7)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    21  36
  10P GAIN WILD-TYPE 207 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     21   36
  10P GAIN WILD-TYPE  207  248
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               21                207
  MALE                 36                248
[1] 2 2
[1] FALSE
D18V4, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    12  42
  10P GAIN WILD-TYPE 172 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12   42
  10P GAIN WILD-TYPE  172  251
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                12                172
  YES               42                251
[1] 2 2
[1] FALSE
D18V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10P GAIN MUTATED            32               17                 8
  10P GAIN WILD-TYPE         162              112               181
D18V6, multiclass
                   clus
vv                  10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASTROCYTOMA                     32                162
  OLIGOASTROCYTOMA                17                112
  OLIGODENDROGLIOMA                8                181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           2    54
  10P GAIN WILD-TYPE                        19   418
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                       2                 19
  WHITE                                          54                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"
D18V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     6  45
  10P GAIN WILD-TYPE  26 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6   45
  10P GAIN WILD-TYPE   26  401
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 26
  NOT HISPANIC OR LATINO               45                401
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    10   2
  10Q GAIN WILD-TYPE 378 119
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                497 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                119 
$`10Q GAIN MUTATED`
TCGA-CS-5393 TCGA-DB-5277 TCGA-DU-A5TS TCGA-E1-A7YI TCGA-FG-A87N TCGA-HT-7476 
       40.18        50.86        31.69         3.65        18.64         6.54 
TCGA-HT-8106 TCGA-P5-A780 TCGA-RY-A83Z TCGA-S9-A7J0 TCGA-S9-A89Z TCGA-TQ-A7RV 
        0.10         2.37         9.90        20.02        20.48        61.41 

$`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        46.95         7.56        49.94        49.12 
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 
       91.13        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 
       63.88        46.06         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        23.21        17.46        13.71 
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         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       154.36        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        33.27        29.85        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
       22.29        11.41        26.76        17.16        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       38.89         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-A7YD 
       57.93       134.27        78.21        95.57       130.78        14.30 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
       29.13        93.21        19.46        12.43        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       23.90        75.02        51.88        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       39.48         0.23         0.20        47.77        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        42.54        41.33        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        28.34 
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        21.53        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87Q 
       28.54        10.78        36.66        48.69        20.45         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-7477 TCGA-HT-7478 
        0.03        16.54         3.75        17.42        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-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-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-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R 
        7.56        12.23        19.20         3.45         4.41        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-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
       30.87         5.46        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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       85.55        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       23.51        19.99         8.19         2.04        20.68        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       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        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        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-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       26.99        31.36        43.04        43.20        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        7.89        39.16        20.02        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 
             61.41             211.17 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             19.33              21.01 
[1] "0.1 - 61.4 (19.3)"  "0.0 - 211.2 (21.0)"
[1] "hr=" "1.1"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5   7
  10Q GAIN WILD-TYPE 223 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    7
  10Q GAIN WILD-TYPE  223  277
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                5                223
  MALE                  7                277
[1] 2 2
[1] FALSE
D19V4, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   9
  10Q GAIN WILD-TYPE 181 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    9
  10Q GAIN WILD-TYPE  181  284
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 3                181
  YES                9                284
[1] 2 2
[1] FALSE
D19V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10Q GAIN MUTATED            10                0                 2
  10Q GAIN WILD-TYPE         184              129               187
D19V6, multiclass
                   clus
vv                  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASTROCYTOMA                     10                184
  OLIGOASTROCYTOMA                 0                129
  OLIGODENDROGLIOMA                2                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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    10
  10Q GAIN WILD-TYPE                        20   462
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                 20
  WHITE                                          10                462
[1] 4 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     2   9
  10Q GAIN WILD-TYPE  30 437
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    9
  10Q GAIN WILD-TYPE   30  437
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 30
  NOT HISPANIC OR LATINO                9                437
[1] 2 2
[1] FALSE

Clustering(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    27   4
  11P GAIN WILD-TYPE 361 117
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                478 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                117 
$`11P GAIN MUTATED`
TCGA-CS-5396 TCGA-CS-6666 TCGA-DB-A4X9 TCGA-DB-A64L TCGA-DH-5144 TCGA-DH-A66D 
        9.96        46.95        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        24.99        22.29        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-A7RN TCGA-TQ-A7RW 
       41.10        35.38        38.56        28.37        33.73        26.99 
TCGA-VM-A8CA 
       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        49.94        49.12         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 
       91.13        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        63.88        46.06 
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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        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        33.27        29.85        31.69 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       24.43        26.17        33.96        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
       20.98        11.41        26.76        17.16        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       38.89         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-A7YD 
       57.93       134.27        78.21        95.57       130.78        14.30 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       29.13        93.21         3.65        19.46        12.43        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU 
       21.30        23.90        75.02        51.88        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       32.35        39.48         0.23         0.20        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        42.54        41.33        18.44 
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        28.34        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        21.53        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        18.64         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-7477 TCGA-HT-7478 
        0.03        16.54        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-7686 
       14.27         0.16        16.24         0.76        44.68        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-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        2.50        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-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       10.52        11.05         0.10        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        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 
        7.99         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         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       19.20         3.45         2.37         4.41        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 
       28.14        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
      135.22        85.55        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        18.54        27.16       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        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       36.69        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
       61.41        31.36        43.04        43.20         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  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 
             24.20              20.76 
[1] "1.2 - 211.2 (24.2)" "0.0 - 182.3 (20.8)"
[1] "hr=" "1.8"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    17  14
  11P GAIN WILD-TYPE 211 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     17   14
  11P GAIN WILD-TYPE  211  270
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               17                211
  MALE                 14                270
[1] 2 2
[1] FALSE
D20V4, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    15  15
  11P GAIN WILD-TYPE 169 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     15   15
  11P GAIN WILD-TYPE  169  278
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                15                169
  YES               15                278
[1] 2 2
[1] FALSE
D20V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11P GAIN MUTATED             4               10                17
  11P GAIN WILD-TYPE         190              119               172
D20V6, multiclass
                   clus
vv                  11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASTROCYTOMA                      4                190
  OLIGOASTROCYTOMA                10                119
  OLIGODENDROGLIOMA               17                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"
                    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    29
  11P GAIN WILD-TYPE                        20   443
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                 20
  WHITE                                          29                443
[1] 4 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     3  27
  11P GAIN WILD-TYPE  29 419
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3   27
  11P GAIN WILD-TYPE   29  419
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 29
  NOT HISPANIC OR LATINO               27                419
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    48  10
  11Q GAIN WILD-TYPE 340 111
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                58                451 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                111 
$`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        17.46       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        24.43        24.99        22.29        47.77 
TCGA-FG-7634 TCGA-FG-A60L TCGA-HT-7474 TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7607 
       15.35        21.53         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        45.60 
TCGA-HW-8319 TCGA-P5-A72W TCGA-QH-A65S TCGA-QH-A65X TCGA-QH-A6CZ TCGA-RY-A840 
       39.75        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        41.10        35.38        75.25        38.56        19.99 
TCGA-S9-A7QY TCGA-S9-A89Z TCGA-TM-A84J TCGA-TQ-A7RJ TCGA-TQ-A7RN TCGA-TQ-A7RW 
       28.37        20.48        24.16        40.41        33.73        26.99 
TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-WY-A85B TCGA-WY-A85C 
       43.04        13.51        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        46.95         7.56        49.94        49.12 
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 
       91.13        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        63.88        46.06        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        23.21        13.71        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         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        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        33.27        29.85        31.69        26.17 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K 
       33.96        25.55        21.57        95.11        20.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76        17.16        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       75.02        51.88        15.32         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
      146.14        13.08        73.48       145.05        32.35        39.48 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        25.48        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 
       14.93        42.54        41.33        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        28.34        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-A6IZ 
       18.38        18.71        23.70        14.76        17.82        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        18.64         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-7475 
       11.54        40.11         0.13         0.03        16.54        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-7602 TCGA-HT-7603 TCGA-HT-7605 
      106.95       172.77         4.01        29.85        23.18         4.57 
TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
       17.29        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-7686 
       14.27         0.16        16.24         0.76        44.68        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 
        0.10        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-8110 
       12.23         6.25         0.10         0.46         2.50        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-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74L 
       21.40        17.52        17.65         2.43        10.52        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 
        0.10        56.58        13.45        41.49        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       35.44        40.01        42.54         6.18        10.55        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         7.99         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X 
        5.88         7.63         0.76         1.28         0.23        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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        28.14 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93         5.85       123.65       135.22        85.55 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
       14.07        36.13         7.92        26.93        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        20.68        15.06        18.54        27.16 
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        54.77        48.33        49.32        34.78        65.39 
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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RK 
       23.80        21.37        19.69        15.98         2.04        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       36.69        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       61.41        31.36        43.20         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        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-A85D 
       51.06        13.32        43.96        39.88        43.40        37.71 
TCGA-WY-A85E 
       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 
             24.18              20.68 
[1] "1.2 - 211.2 (24.2)" "0.0 - 172.8 (20.7)"
[1] "hr=" "1.6"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    30  28
  11Q GAIN WILD-TYPE 198 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     30   28
  11Q GAIN WILD-TYPE  198  256
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               30                198
  MALE                 28                256
[1] 2 2
[1] FALSE
D21V4, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    23  34
  11Q GAIN WILD-TYPE 161 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     23   34
  11Q GAIN WILD-TYPE  161  259
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                23                161
  YES               34                259
[1] 2 2
[1] FALSE
D21V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11Q GAIN MUTATED            17               14                27
  11Q GAIN WILD-TYPE         177              115               162
D21V6, multiclass
                   clus
vv                  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASTROCYTOMA                     17                177
  OLIGOASTROCYTOMA                14                115
  OLIGODENDROGLIOMA               27                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"
                    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    53
  11Q GAIN WILD-TYPE                        19   419
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                 19
  WHITE                                          53                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"
D21V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  48
  11Q GAIN WILD-TYPE  28 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   48
  11Q GAIN WILD-TYPE   28  398
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 28
  NOT HISPANIC OR LATINO               48                398
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    21  12
  12P GAIN WILD-TYPE 367 109
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                33                476 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                12                109 
$`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        24.43        26.17        33.96 
TCGA-DU-A7T8 TCGA-DU-A7TI TCGA-E1-5304 TCGA-E1-A7YQ TCGA-E1-A7YW TCGA-FG-7634 
      139.04        38.89        41.13        51.88        36.82        15.35 
TCGA-FG-8182 TCGA-FG-8191 TCGA-HT-7469 TCGA-HT-7473 TCGA-HT-7604 TCGA-HT-7873 
       13.68        32.61        11.54        16.54       122.47        23.61 
TCGA-HT-7884 TCGA-HT-8018 TCGA-HT-A614 TCGA-QH-A6CV TCGA-S9-A7IZ TCGA-TM-A84I 
       11.28        37.87         2.70        14.53        19.99        28.08 
TCGA-TQ-A7RR TCGA-WY-A858 TCGA-WY-A85E 
       25.87        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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 
       49.12         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 
       91.13        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        63.88        46.06 
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 
       23.21        17.46        13.71        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 
        2.40        11.47       156.23       154.36        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        33.27        29.85        31.69        24.99        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       21.57        95.11        20.98        22.29        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       17.16        21.30        17.98        84.33        51.52        37.38 
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-A7YD 
       57.93       134.27        78.21        95.57       130.78        14.30 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       29.13        93.21         3.65        19.46        12.43        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       21.30        23.90        75.02        15.32         0.76        32.45 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
      146.14        13.08        73.48       145.05        32.35        39.48 
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        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        42.54        41.33        18.44        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8186 
       22.55        20.61        20.09        28.34        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        14.96        22.52        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        21.53        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        18.64         5.72        27.52         0.10         6.67 
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-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-7605 
      172.77         4.01         5.03        29.85        23.18         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-7874 
       19.23        39.09         0.23        50.63         0.49        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-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-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-A615 TCGA-HT-A616 TCGA-HT-A617 
       27.35         0.10         5.33        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        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        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 
        7.99         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         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       19.20         3.45         2.37         4.41        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW 
       12.62        15.85        14.04        19.33        14.83        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        41.10        28.14        35.38        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       24.39        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       18.64        14.07        36.13         7.92        26.93        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        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       31.20        30.05        26.14        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 
            139.04             211.17 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            30.120             20.465 
[1] "1.2 - 139.0 (30.1)" "0.0 - 211.2 (20.5)"
[1] "hr=" "1.3"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    11  22
  12P GAIN WILD-TYPE 217 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     11   22
  12P GAIN WILD-TYPE  217  262
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               11                217
  MALE                 22                262
[1] 2 2
[1] FALSE
D22V4, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     6  25
  12P GAIN WILD-TYPE 178 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6   25
  12P GAIN WILD-TYPE  178  268
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 6                178
  YES               25                268
[1] 2 2
[1] FALSE
D22V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12P GAIN MUTATED            11               12                10
  12P GAIN WILD-TYPE         183              117               179
D22V6, multiclass
                   clus
vv                  12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASTROCYTOMA                     11                183
  OLIGOASTROCYTOMA                12                117
  OLIGODENDROGLIOMA               10                179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           2    30
  12P GAIN WILD-TYPE                        19   442
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                       2                 19
  WHITE                                          30                442
[1] 4 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     2  29
  12P GAIN WILD-TYPE  30 417
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   29
  12P GAIN WILD-TYPE   30  417
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 30
  NOT HISPANIC OR LATINO               29                417
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED     7   9
  12Q GAIN WILD-TYPE 381 112
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                493 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 9                112 
$`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        24.43 
TCGA-DU-A5TY TCGA-DU-A7TA TCGA-DU-A7TI TCGA-E1-5304 TCGA-E1-A7YQ TCGA-FG-7634 
       33.96        84.33        38.89        41.13        51.88        15.35 
TCGA-HT-7873 TCGA-HT-7884 TCGA-QH-A6CV TCGA-S9-A6UA 
       23.61        11.28        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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        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         2.40        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       29.85        31.69        26.17        24.99        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       95.11        20.98        22.29        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       21.30        17.98       139.04        51.52        37.38         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-A7YD TCGA-E1-A7YE 
      134.27        78.21        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
       93.21         3.65        19.46        12.43        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       23.90        75.02        15.32         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
      146.14        13.08        73.48       145.05        32.35        39.48 
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        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        42.54        41.33        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        28.34        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 
       21.53        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        18.64         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-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-7902 
        0.13         3.68         5.33        35.47         3.72        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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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-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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       18.64        14.07        36.13         7.92        26.93        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       19.99        20.02         8.19         2.04        20.68        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       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        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       36.69        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        43.04        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        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 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.22               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             84.33             211.17 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             27.32              20.71 
[1] "1.2 - 84.3 (27.3)"  "0.0 - 211.2 (20.7)"
[1] "hr=" "2.5"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     5  11
  12Q GAIN WILD-TYPE 223 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5   11
  12Q GAIN WILD-TYPE  223  273
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                5                223
  MALE                 11                273
[1] 2 2
[1] FALSE
D23V4, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4  11
  12Q GAIN WILD-TYPE 180 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4   11
  12Q GAIN WILD-TYPE  180  282
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 4                180
  YES               11                282
[1] 2 2
[1] FALSE
D23V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12Q GAIN MUTATED             6                3                 7
  12Q GAIN WILD-TYPE         188              126               182
D23V6, multiclass
                   clus
vv                  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASTROCYTOMA                      6                188
  OLIGOASTROCYTOMA                 3                126
  OLIGODENDROGLIOMA                7                182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           1    14
  12Q GAIN WILD-TYPE                        20   458
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                       1                 20
  WHITE                                          14                458
[1] 4 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  16
  12Q GAIN WILD-TYPE  32 430
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   16
  12Q GAIN WILD-TYPE   32  430
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO               16                430
[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 383 121
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                504 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                121 
$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       31.69        24.43        26.17        24.99        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       21.57        95.11        20.98        22.29        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       17.16        21.30        17.98       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       95.57       130.78        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       51.88        15.32         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         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        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        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 
       21.53        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        18.64         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-7616 TCGA-HT-7620 
        3.16        22.06        45.99        56.09         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-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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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        41.10        28.14        35.38        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       24.39        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       18.64        14.07        36.13         7.92        26.93        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       19.99        20.02         8.19         2.04        20.68        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       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        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       36.69        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        43.04        43.20 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        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 

  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 
            13.510             20.995 
[1] "1.9 - 57.6 (13.5)"  "0.0 - 211.2 (21.0)"
[1] "hr="     "3300000"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     3   3
  13Q GAIN WILD-TYPE 225 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    3
  13Q GAIN WILD-TYPE  225  281
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                3                225
  MALE                  3                281
[1] 2 2
[1] FALSE
D24V4, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     5   1
  13Q GAIN WILD-TYPE 179 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    1
  13Q GAIN WILD-TYPE  179  292
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 5                179
  YES                1                292
[1] 2 2
[1] FALSE
D24V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  13Q GAIN MUTATED             2                2                 2
  13Q GAIN WILD-TYPE         192              127               187
D24V6, multiclass
                   clus
vv                  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASTROCYTOMA                      2                192
  OLIGOASTROCYTOMA                 2                127
  OLIGODENDROGLIOMA                2                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                        21   467
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                 21
  WHITE                                           5                467
[1] 4 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  32 441
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    5
  13Q GAIN WILD-TYPE   32  441
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO                5                441
[1] 2 2
[1] FALSE

Clustering(25) Variable = 14Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     2   2
  14Q GAIN WILD-TYPE 386 119
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                505 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                119 
$`14Q GAIN MUTATED`
TCGA-CS-6665 TCGA-DH-A669 TCGA-DU-7019 TCGA-TQ-A8XE 
       12.43        30.21        26.30        31.36 

$`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        46.95         7.56        49.94        49.12 
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        91.13        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        63.88        46.06         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        23.21        17.46        13.71 
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         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       154.36        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        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
       22.29        11.41        26.76        17.16        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       38.89         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-A7YD 
       57.93       134.27        78.21        95.57       130.78        14.30 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       29.13        93.21         3.65        19.46        12.43        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU 
       21.30        23.90        75.02        51.88        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         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 
       52.21        36.82        18.77        14.93        42.54        41.33 
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 
       28.34        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        21.53        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 
       18.64         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-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        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        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 
        7.99         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         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       19.20         3.45         2.37         4.41        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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       85.55        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        18.54        28.37        27.16       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        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       25.87        33.93        61.41        26.99        43.04        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        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 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             12.43               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             31.36             211.17 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            28.255             20.810 
[1] "12.4 - 31.4 (28.3)" "0.0 - 211.2 (20.8)"
[1] "hr=" "3"  
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   2
  14Q GAIN WILD-TYPE 226 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    2
  14Q GAIN WILD-TYPE  226  282
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                2                226
  MALE                  2                282
[1] 2 2
[1] FALSE
D25V4, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   2
  14Q GAIN WILD-TYPE 182 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    2
  14Q GAIN WILD-TYPE  182  291
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 2                182
  YES                2                291
[1] 2 2
[1] FALSE
D25V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  14Q GAIN MUTATED             1                1                 2
  14Q GAIN WILD-TYPE         193              128               187
D25V6, multiclass
                   clus
vv                  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASTROCYTOMA                      1                193
  OLIGOASTROCYTOMA                 1                128
  OLIGODENDROGLIOMA                2                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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     4
  14Q GAIN WILD-TYPE                        21   468
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                 21
  WHITE                                           4                468
[1] 4 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     1   3
  14Q GAIN WILD-TYPE  31 443
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    3
  14Q GAIN WILD-TYPE   31  443
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 31
  NOT HISPANIC OR LATINO                3                443
[1] 2 2
[1] FALSE

Clustering(26) Variable = 15Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     5   6
  15Q GAIN WILD-TYPE 383 115
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                498 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                115 
$`15Q GAIN MUTATED`
TCGA-CS-4943 TCGA-DU-5852 TCGA-DU-7014 TCGA-DU-7306 TCGA-E1-5304 TCGA-E1-A7YQ 
       18.15         6.74       117.40        41.98        41.13        51.88 
TCGA-E1-A7YV TCGA-HT-7477 TCGA-P5-A780 TCGA-S9-A6UA TCGA-S9-A7IZ 
       32.45        24.26         2.37         5.85        19.99 

$`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        46.95         7.56        49.94        49.12 
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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
       13.71        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         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       154.36        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 
       33.27        29.85        31.69        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76        17.16        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       75.02        15.32         0.76        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         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        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        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        21.53 
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        18.64         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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       12.23        19.20         3.45         4.41        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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       18.64        14.07        36.13         7.92        26.93        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        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        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-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        43.04        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        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 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              2.37               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            117.40             211.17 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             24.26              20.81 
[1] "2.4 - 117.4 (24.3)" "0.0 - 211.2 (20.8)"
[1] "hr=" "2.2"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     5   6
  15Q GAIN WILD-TYPE 223 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      5    6
  15Q GAIN WILD-TYPE  223  278
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                5                223
  MALE                  6                278
[1] 2 2
[1] FALSE
D26V4, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3   8
  15Q GAIN WILD-TYPE 181 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    8
  15Q GAIN WILD-TYPE  181  285
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 3                181
  YES                8                285
[1] 2 2
[1] FALSE
D26V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  15Q GAIN MUTATED             6                3                 2
  15Q GAIN WILD-TYPE         188              126               187
D26V6, multiclass
                   clus
vv                  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASTROCYTOMA                      6                188
  OLIGOASTROCYTOMA                 3                126
  OLIGODENDROGLIOMA                2                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           1    10
  15Q GAIN WILD-TYPE                        20   462
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                       1                 20
  WHITE                                          10                462
[1] 4 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  10
  15Q GAIN WILD-TYPE  32 436
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   10
  15Q GAIN WILD-TYPE   32  436
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO               10                436
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    11   6
  16P GAIN WILD-TYPE 377 115
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                17                492 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                115 
$`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-E1-A7YD TCGA-FG-5962 TCGA-HT-A5R7 
       14.99        31.69        41.13        14.30        47.77        20.22 
TCGA-HT-A618 TCGA-S9-A6WH TCGA-S9-A7QW TCGA-TM-A84I TCGA-VM-A8CA 
       16.83        38.56        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        46.95         7.56        49.94        49.12 
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        91.13        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 
       63.88        46.06         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        23.21        17.46        13.71        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         2.40        11.47       156.23       154.36 
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        33.27        29.85        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       26.17        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
       20.98        22.29        11.41        26.76        17.16        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
       44.42        38.89         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-A7YE 
       57.93       134.27        78.21        95.57       130.78        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
       93.21         3.65        19.46        12.43        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       23.90        75.02        51.88        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       39.48         0.23         0.20        25.48        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        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        28.34        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        21.53        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        18.64         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-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-A619 TCGA-HT-A61B TCGA-HT-A61C 
       16.93         1.81        16.14        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        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       75.25       135.22        85.55        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       26.93        23.51        19.99        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       20.68        18.54        28.37        27.16       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        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       36.69        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        43.04        43.20 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        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 

  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 
             28.08              20.81 
[1] "1.2 - 211.2 (28.1)" "0.0 - 182.3 (20.8)"
[1] "hr=" "1.2"
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     9   8
  16P GAIN WILD-TYPE 219 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    8
  16P GAIN WILD-TYPE  219  276
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                9                219
  MALE                  8                276
[1] 2 2
[1] FALSE
D27V4, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     4  12
  16P GAIN WILD-TYPE 180 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4   12
  16P GAIN WILD-TYPE  180  281
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                180
  YES               12                281
[1] 2 2
[1] FALSE
D27V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16P GAIN MUTATED            11                2                 4
  16P GAIN WILD-TYPE         183              127               185
D27V6, multiclass
                   clus
vv                  16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASTROCYTOMA                     11                183
  OLIGOASTROCYTOMA                 2                127
  OLIGODENDROGLIOMA                4                185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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    15
  16P GAIN WILD-TYPE                        20   457
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                 20
  WHITE                                          15                457
[1] 4 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  16
  16P GAIN WILD-TYPE  32 430
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   16
  16P GAIN WILD-TYPE   32  430
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO               16                430
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    12   7
  16Q GAIN WILD-TYPE 376 114
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                490 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                114 
$`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-E1-A7YD TCGA-FG-5962 TCGA-HT-A5R7 
       31.69        50.14        41.13        14.30        47.77        20.22 
TCGA-HT-A616 TCGA-HT-A618 TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-TM-A84I TCGA-TM-A84Q 
        1.81        16.83        20.02        15.06        28.08        25.38 
TCGA-VM-A8CA 
       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        46.95         7.56        49.94        49.12 
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        91.13        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 
       63.88        46.06         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        23.21        17.46        13.71 
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         2.40        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
      154.36       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        33.27        29.85 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       24.43        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       95.11        20.98        22.29        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 
        7.50        44.42        38.89         0.56        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE 
       57.93       134.27        78.21        95.57       130.78        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
       93.21         3.65        19.46        12.43        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       23.90        75.02        51.88        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       39.48         0.23         0.20        25.48        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        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        28.34        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        21.53        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        18.64         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-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-A617 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.93        16.14        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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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        41.10        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       26.93        23.51        19.99         8.19         2.04        20.68 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       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        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        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-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       33.24        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        31.36        43.04        43.20         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  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 
            20.220             20.895 
[1] "1.2 - 211.2 (20.2)" "0.0 - 182.3 (20.9)"
[1] "hr=" "1.4"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    10   9
  16Q GAIN WILD-TYPE 218 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    9
  16Q GAIN WILD-TYPE  218  275
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               10                218
  MALE                  9                275
[1] 2 2
[1] FALSE
D28V4, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     5  13
  16Q GAIN WILD-TYPE 179 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5   13
  16Q GAIN WILD-TYPE  179  280
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 5                179
  YES               13                280
[1] 2 2
[1] FALSE
D28V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16Q GAIN MUTATED            13                1                 5
  16Q GAIN WILD-TYPE         181              128               184
D28V6, multiclass
                   clus
vv                  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASTROCYTOMA                     13                181
  OLIGOASTROCYTOMA                 1                128
  OLIGODENDROGLIOMA                5                184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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    17
  16Q GAIN WILD-TYPE                        20   455
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                 20
  WHITE                                          17                455
[1] 4 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  18
  16Q GAIN WILD-TYPE  32 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   18
  16Q GAIN WILD-TYPE   32  428
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO               18                428
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    12   8
  17P GAIN WILD-TYPE 376 113
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                489 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                113 
$`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        20.98        41.13 
TCGA-E1-A7YD TCGA-E1-A7YS TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A6J3 TCGA-HT-7477 
       14.30        15.32        47.77        15.35        22.26        24.26 
TCGA-IK-7675 TCGA-QH-A6CV TCGA-S9-A6TS TCGA-S9-A6U1 TCGA-S9-A6WL TCGA-TM-A84M 
       19.00        14.53        62.17        25.81        31.10        24.79 
TCGA-VM-A8CA TCGA-VW-A8FI 
       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        46.95         7.56        49.94        49.12 
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        91.13        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        63.88        46.06         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        23.21        17.46        13.71        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         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       154.36        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 
       33.27        29.85        31.69        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       33.96        25.55        21.57        95.11        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76        17.16        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
       95.57       130.78        29.13        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ 
       12.43        16.18        21.30        23.90        75.02        51.88 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
        0.76        32.45        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
      145.05        32.35        39.48         0.23         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       52.21        36.82        18.77        14.93        42.54        41.33 
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        28.34 
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-A70Y 
       14.76        17.82        21.53        15.02        16.44        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        18.64         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 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        87.12        18.77        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       36.82        24.39        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       38.56        84.99        19.86        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O 
       40.64        30.44        28.08        24.16        40.83        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        31.36        43.04        43.20         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              8.05               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             62.17             211.17 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             19.99              20.81 
[1] "8.1 - 62.2 (20.0)"  "0.0 - 211.2 (20.8)"
[1] "hr=" "2.7"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     5  15
  17P GAIN WILD-TYPE 223 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5   15
  17P GAIN WILD-TYPE  223  269
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                5                223
  MALE                 15                269
[1] 2 2
[1] FALSE
D29V4, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     6  14
  17P GAIN WILD-TYPE 178 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      6   14
  17P GAIN WILD-TYPE  178  279
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 6                178
  YES               14                279
[1] 2 2
[1] FALSE
D29V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17P GAIN MUTATED            11                1                 8
  17P GAIN WILD-TYPE         183              128               181
D29V6, multiclass
                   clus
vv                  17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASTROCYTOMA                     11                183
  OLIGOASTROCYTOMA                 1                128
  OLIGODENDROGLIOMA                8                181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           1    17
  17P GAIN WILD-TYPE                        20   455
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                       1                 20
  WHITE                                          17                455
[1] 4 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  18
  17P GAIN WILD-TYPE  31 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   18
  17P GAIN WILD-TYPE   31  428
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 31
  NOT HISPANIC OR LATINO               18                428
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    14   9
  17Q GAIN WILD-TYPE 374 112
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                486 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                112 
$`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        20.98 
TCGA-E1-5304 TCGA-E1-A7YD TCGA-E1-A7YS TCGA-FG-5962 TCGA-FG-7634 TCGA-HT-7477 
       41.13        14.30        15.32        47.77        15.35        24.26 
TCGA-IK-7675 TCGA-QH-A6CV TCGA-S9-A6TS TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A6WL 
       19.00        14.53        62.17        25.81         5.85        31.10 
TCGA-TM-A84M TCGA-TQ-A7RK TCGA-VM-A8CA TCGA-VM-A8CH TCGA-VW-A8FI 
       24.79        44.09        13.51        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        46.95         7.56        49.94        49.12 
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        91.13        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 
       63.88        46.06         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        23.21        17.46        13.71        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         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 
      156.23       154.36        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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       25.55        21.57        95.11        22.29        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       17.16        21.30        17.98       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       37.38         7.50        44.42        38.89         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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK 
      130.78        29.13        93.21         3.65        19.46        12.43 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YU 
       16.18        21.30        23.90        75.02        51.88         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       32.35        39.48         0.23         0.20        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        42.54        41.33        18.44 
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        28.34        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        21.53        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        18.64         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 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        87.12        18.77        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       36.82        24.39        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
       95.93       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       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        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        28.08        24.16        40.83        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
        2.04        40.41        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       26.14        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF 
       43.04        43.20         0.10         7.89        39.16        20.02 
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 
             19.00              20.91 
[1] "5.8 - 62.2 (19.0)"  "0.0 - 211.2 (20.9)"
[1] "hr=" "2.7"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6  17
  17Q GAIN WILD-TYPE 222 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6   17
  17Q GAIN WILD-TYPE  222  267
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                6                222
  MALE                 17                267
[1] 2 2
[1] FALSE
D30V4, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    10  13
  17Q GAIN WILD-TYPE 174 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     10   13
  17Q GAIN WILD-TYPE  174  280
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                10                174
  YES               13                280
[1] 2 2
[1] FALSE
D30V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17Q GAIN MUTATED            12                3                 8
  17Q GAIN WILD-TYPE         182              126               181
D30V6, multiclass
                   clus
vv                  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASTROCYTOMA                     12                182
  OLIGOASTROCYTOMA                 3                126
  OLIGODENDROGLIOMA                8                181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           1    19
  17Q GAIN WILD-TYPE                        20   453
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                       1                 20
  WHITE                                          19                453
[1] 4 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     2  18
  17Q GAIN WILD-TYPE  30 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   18
  17Q GAIN WILD-TYPE   30  428
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 30
  NOT HISPANIC OR LATINO               18                428
[1] 2 2
[1] FALSE

Clustering(31) Variable = 18P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     8   9
  18P GAIN WILD-TYPE 380 112
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                492 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                112 
$`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        17.46        14.99        19.13        31.69 
TCGA-DU-A5TY TCGA-E1-5304 TCGA-E1-A7YE TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-HT-8111 
       33.96        41.13        29.13        51.88        32.45         0.23 
TCGA-HW-7489 TCGA-QH-A6CS TCGA-QH-A6X9 TCGA-S9-A89Z TCGA-WY-A85E 
       41.49        19.33         1.91        20.48        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        46.95         7.56        49.94        49.12 
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 
       91.13        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 
       63.88        46.06         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        23.21        13.71        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         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       154.36       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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       29.85        24.43        26.17        24.99        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       95.11        20.98        22.29        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
        7.50        44.42        38.89         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-A7YD TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       14.30        93.21         3.65        19.46        12.43        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW 
       21.30        23.90        75.02        15.32         0.76        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
      146.14        13.08        73.48       145.05        32.35        39.48 
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        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        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        28.34        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        21.53        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        18.64         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 
       56.58        13.45        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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-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-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       14.53        16.34        16.73        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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       85.55        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        18.54        28.37        27.16       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        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       36.69        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        43.04        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        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 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.23               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             51.88             211.17 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            20.810             20.895 
[1] "0.2 - 51.9 (20.8)"  "0.0 - 211.2 (20.9)"
[1] "hr=" "3.1"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     9   8
  18P GAIN WILD-TYPE 219 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      9    8
  18P GAIN WILD-TYPE  219  276
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                9                219
  MALE                  8                276
[1] 2 2
[1] FALSE
D31V4, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     5  12
  18P GAIN WILD-TYPE 179 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5   12
  18P GAIN WILD-TYPE  179  281
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 5                179
  YES               12                281
[1] 2 2
[1] FALSE
D31V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18P GAIN MUTATED             9                4                 4
  18P GAIN WILD-TYPE         185              125               185
D31V6, multiclass
                   clus
vv                  18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASTROCYTOMA                      9                185
  OLIGOASTROCYTOMA                 4                125
  OLIGODENDROGLIOMA                4                185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           2    15
  18P GAIN WILD-TYPE                        19   457
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                       2                 19
  WHITE                                          15                457
[1] 4 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  16
  18P GAIN WILD-TYPE  32 430
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   16
  18P GAIN WILD-TYPE   32  430
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO               16                430
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     5   8
  18Q GAIN WILD-TYPE 383 113
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                496 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                113 
$`18Q GAIN MUTATED`
TCGA-DU-7010 TCGA-DU-8165 TCGA-DU-A5TS TCGA-DU-A5TY TCGA-E1-5304 TCGA-E1-A7YE 
       14.99        19.13        31.69        33.96        41.13        29.13 
TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-HT-8111 TCGA-HW-7489 TCGA-QH-A6CS 
       16.18        51.88        32.45         0.23        41.49        19.33 
TCGA-S9-A89Z 
       20.48 

$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       24.99        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76        17.16        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
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-A7YD TCGA-E1-A7YH TCGA-E1-A7YI 
       78.21        95.57       130.78        14.30        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS 
       19.46        12.43        21.30        23.90        75.02        15.32 
TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
        0.76        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         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 
       52.21        36.82        18.77        14.93        42.54        41.33 
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 
       28.34        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        21.53        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 
       18.64         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-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-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-7490 TCGA-HW-7491 
       11.05         0.10        56.58        13.45        45.60        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54         6.18 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55        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         7.99         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 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        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-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 
       41.10        28.14        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       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        54.77        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 
             51.88             211.17 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             29.13              20.81 
[1] "0.2 - 51.9 (29.1)"  "0.0 - 211.2 (20.8)"
[1] "hr=" "3.4"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     6   7
  18Q GAIN WILD-TYPE 222 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6    7
  18Q GAIN WILD-TYPE  222  277
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                6                222
  MALE                  7                277
[1] 2 2
[1] FALSE
D32V4, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  11
  18Q GAIN WILD-TYPE 182 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   11
  18Q GAIN WILD-TYPE  182  282
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 2                182
  YES               11                282
[1] 2 2
[1] FALSE
D32V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18Q GAIN MUTATED             7                3                 3
  18Q GAIN WILD-TYPE         187              126               186
D32V6, multiclass
                   clus
vv                  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASTROCYTOMA                      7                187
  OLIGOASTROCYTOMA                 3                126
  OLIGODENDROGLIOMA                3                186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           2    11
  18Q GAIN WILD-TYPE                        19   461
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                       2                 19
  WHITE                                          11                461
[1] 4 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  13
  18Q GAIN WILD-TYPE  32 433
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   13
  18Q GAIN WILD-TYPE   32  433
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO               13                433
[1] 2 2
[1] FALSE

Clustering(33) Variable = 19P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    74  24
  19P GAIN WILD-TYPE 314  97
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                98                411 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                24                 97 
$`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        49.94        75.25 
TCGA-DB-5278 TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64R 
       91.13        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       154.36        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        24.43        25.55 
TCGA-DU-A76K TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YO 
       11.41         0.56        41.13        19.46        16.18        75.02 
TCGA-E1-A7YS TCGA-FG-5962 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8186 TCGA-FG-8188 
       15.32        47.77        18.44        20.09        16.01        14.96 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60K TCGA-FG-A87Q TCGA-HT-7468 TCGA-HT-7469 
       10.72        18.38        17.82         5.72         6.67        11.54 
TCGA-HT-7480 TCGA-HT-7687 TCGA-HT-7695 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7875 
       75.19         0.10        14.53         0.49        23.61         0.33 
TCGA-HT-7882 TCGA-HT-8012 TCGA-HT-8104 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 
        3.72         9.40        12.23        27.35         5.33        16.93 
TCGA-HT-A61B TCGA-HW-7495 TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-P5-A72U TCGA-P5-A730 
       17.52        35.44        14.40         4.11         0.23        10.95 
TCGA-QH-A65X TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK 
       15.85        14.53         9.17         5.03        11.08        88.83 
TCGA-R8-A6ML TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-S9-A6TV TCGA-S9-A6TY 
       94.03        59.38        30.87         5.46        18.77        35.38 
TCGA-S9-A6U2 TCGA-S9-A6WE TCGA-S9-A6WM TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QZ 
       29.85       135.22        19.86         8.19         2.04        27.16 
TCGA-S9-A7R1 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84G TCGA-TQ-A7RG TCGA-TQ-A7RI 
      169.84        54.77        24.92        40.64        19.69         2.04 
TCGA-TQ-A7RN TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       33.73        30.05        26.14        13.51         0.10        39.16 
TCGA-VW-A7QS TCGA-W9-A837 
       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        46.95 
TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        7.56        49.12         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        63.88        46.06         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        23.21        17.46        13.71        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         2.40        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 
       33.27        29.85        31.69        26.17        24.99        33.96 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76O 
       21.57        95.11        20.98        22.29        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.50        44.42        38.89        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD 
       57.93       134.27        78.21        95.57       130.78        14.30 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YN 
       29.13        93.21         3.65        12.43        21.30        23.90 
TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       51.88         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 
       41.33        15.35        17.88        22.55        20.61        28.34 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       13.68        14.24        20.09        22.52        32.61        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        23.70        14.76        21.53        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-FN-7833 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
       18.64        27.52         0.10        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-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-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-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-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
        6.90        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
       37.15         0.13         3.68         5.33        35.47        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-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-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-A5RB 
        0.23        26.04         0.13        20.22         0.07         0.10 
TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C 
        2.70         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        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 
       13.45        41.49        45.60        68.32        69.27        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        42.77        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        7.99         2.37         2.30         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A731 TCGA-P5-A733 
        1.28        10.42        13.25        11.64         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS 
        4.41        15.16         2.53        12.62        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.83        13.61        12.23         2.20        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A870 TCGA-R8-A6MO 
       16.34        16.73         1.91        16.50        12.99        32.65 
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-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       87.12        41.10        28.14        36.82        24.39        25.81 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       75.25        85.55        38.56        84.99        31.10        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       23.51        19.99        20.02        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       28.37        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       18.71        20.48        48.33        49.32        34.78        65.39 
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-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-A7RF TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RO 
       21.37        15.98        40.41        44.09        36.69        31.20 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       25.87        33.93        61.41        26.99        31.36        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
       43.20         7.89        20.02        23.47        37.05        16.01 
TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        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 

  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 
            19.575             21.300 
[1] "0.1 - 169.8 (19.6)" "0.0 - 211.2 (21.3)"
[1] "hr=" "1.1"
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    39  61
  19P GAIN WILD-TYPE 189 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     39   61
  19P GAIN WILD-TYPE  189  223
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               39                189
  MALE                 61                223
[1] 2 2
[1] FALSE
D33V4, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    44  49
  19P GAIN WILD-TYPE 140 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     44   49
  19P GAIN WILD-TYPE  140  244
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                44                140
  YES               49                244
[1] 2 2
[1] FALSE
D33V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19P GAIN MUTATED            20               19                61
  19P GAIN WILD-TYPE         174              110               128
D33V6, multiclass
                   clus
vv                  19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASTROCYTOMA                     20                174
  OLIGOASTROCYTOMA                19                110
  OLIGODENDROGLIOMA               61                128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           6    89
  19P GAIN WILD-TYPE                        15   383
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                       6                 15
  WHITE                                          89                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"
D33V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    10  86
  19P GAIN WILD-TYPE  22 360
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     10   86
  19P GAIN WILD-TYPE   22  360
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                   10                 22
  NOT HISPANIC OR LATINO               86                360
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    14  11
  19Q GAIN WILD-TYPE 374 110
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                25                484 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                110 
$`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-E1-A7YJ TCGA-E1-A7YL TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-A4MU 
        0.56        19.46        16.18        18.44        20.09        10.72 
TCGA-FG-A4MW TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7882 TCGA-HT-8104 TCGA-HT-A5RA 
       18.38         0.49        23.61         3.72        12.23        27.35 
TCGA-KT-A7W1 TCGA-P5-A72U TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6WM TCGA-TM-A7C3 
       14.40         0.23        14.53         5.03        19.86        54.77 
TCGA-TQ-A7RP 
       30.05 

$`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        46.95         7.56        49.94        49.12         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 
       91.13        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 
       63.88        46.06         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        23.21        17.46        13.71 
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         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L 
       25.55        21.57        95.11        20.98        22.29        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       17.16        21.30        17.98       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 
       37.38         7.50        44.42        38.89        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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK 
      130.78        14.30        29.13        93.21         3.65        12.43 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU 
       21.30        23.90        75.02        51.88        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         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 
       52.21        36.82        18.77        14.93        42.54        41.33 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 
       15.35        17.88        22.55        20.61        28.34        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-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       38.27        18.71        23.70        14.76        17.82        21.53 
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        18.64         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-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-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.23        50.63        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47        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-8105 
        9.40        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-A5RC TCGA-HT-A614 
        0.13        20.22         0.07         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 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         7.99         2.37         2.30         4.11 
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-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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        41.10        28.14        35.38        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       24.39        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       38.56        84.99        31.10        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        31.59        18.71        20.48        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       31.20        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 
              0.23               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             54.77             211.17 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            16.830             21.465 
[1] "0.2 - 54.8 (16.8)"  "0.0 - 211.2 (21.5)"
[1] "hr=" "4.8"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     9  16
  19Q GAIN WILD-TYPE 219 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9   16
  19Q GAIN WILD-TYPE  219  268
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                9                219
  MALE                 16                268
[1] 2 2
[1] FALSE
D34V4, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     4  17
  19Q GAIN WILD-TYPE 180 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4   17
  19Q GAIN WILD-TYPE  180  276
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 4                180
  YES               17                276
[1] 2 2
[1] FALSE
D34V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19Q GAIN MUTATED            11                9                 5
  19Q GAIN WILD-TYPE         183              120               184
D34V6, multiclass
                   clus
vv                  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASTROCYTOMA                     11                183
  OLIGOASTROCYTOMA                 9                120
  OLIGODENDROGLIOMA                5                184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           3    21
  19Q GAIN WILD-TYPE                        18   451
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                       3                 18
  WHITE                                          21                451
[1] 4 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     2  22
  19Q GAIN WILD-TYPE  30 424
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   22
  19Q GAIN WILD-TYPE   30  424
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 30
  NOT HISPANIC OR LATINO               22                424
[1] 2 2
[1] FALSE

Clustering(35) Variable = 20P GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    22  21
  20P GAIN WILD-TYPE 366 100
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                43                466 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                21                100 
$`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        24.43        33.96        20.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-E1-5304 TCGA-E1-A7YD TCGA-E1-A7YJ TCGA-E1-A7YL 
       11.41        26.76        41.13        14.30        19.46        16.18 
TCGA-E1-A7YQ TCGA-E1-A7Z2 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A4MU TCGA-HT-7474 
       51.88        13.08        47.77        15.35        10.72         3.75 
TCGA-HT-7477 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8104 TCGA-HT-A5RC TCGA-HT-A74H 
       24.26         0.49         3.72        12.23         5.33         2.43 
TCGA-HW-A5KK TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6WH TCGA-S9-A6WM TCGA-TM-A7C3 
       12.76        14.53         5.03        38.56        19.86        54.77 
TCGA-VM-A8CA 
       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        46.95 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
        7.56        49.94        49.12         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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
       13.71        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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85        31.69        26.17        24.99 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R 
       25.55        21.57        95.11        22.29        17.16        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
       44.42        38.89         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-A7YE 
       57.93       134.27        78.21        95.57       130.78        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       93.21         3.65        12.43        21.30        23.90        75.02 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 
       15.32         0.76        32.45        36.82       146.14        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
      145.05        32.35        39.48         0.23         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       52.21        36.82        18.77        14.93        42.54        41.33 
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        28.34 
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        21.53        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        18.64         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 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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-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-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       85.55        84.99        31.10        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        31.59        18.71        20.48        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        31.36        43.04        43.20         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.49               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             54.77             211.17 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             16.18              21.55 
[1] "0.5 - 54.8 (16.2)"  "0.0 - 211.2 (21.6)"
[1] "hr=" "4.7"
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    20  23
  20P GAIN WILD-TYPE 208 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     20   23
  20P GAIN WILD-TYPE  208  261
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               20                208
  MALE                 23                261
[1] 2 2
[1] FALSE
D35V4, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     9  30
  20P GAIN WILD-TYPE 175 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      9   30
  20P GAIN WILD-TYPE  175  263
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 9                175
  YES               30                263
[1] 2 2
[1] FALSE
D35V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20P GAIN MUTATED            22                8                13
  20P GAIN WILD-TYPE         172              121               176
D35V6, multiclass
                   clus
vv                  20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASTROCYTOMA                     22                172
  OLIGOASTROCYTOMA                 8                121
  OLIGODENDROGLIOMA               13                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"
                    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                           3    38
  20P GAIN WILD-TYPE                        18   434
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                       3                 18
  WHITE                                          38                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"
D35V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1  39
  20P GAIN WILD-TYPE  31 407
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   39
  20P GAIN WILD-TYPE   31  407
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 31
  NOT HISPANIC OR LATINO               39                407
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    22  21
  20Q GAIN WILD-TYPE 366 100
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                466 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                21                100 
$`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        24.43        33.96        20.98        11.41 
TCGA-DU-A76L TCGA-E1-5304 TCGA-E1-A7YD TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YQ 
       26.76        41.13        14.30        19.46        16.18        51.88 
TCGA-E1-A7Z2 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A4MU TCGA-HT-7477 TCGA-HT-7693 
       13.08        47.77        15.35        10.72        24.26        17.52 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8104 TCGA-HT-8563 TCGA-HT-A5RC TCGA-HT-A74H 
        0.49         3.72        12.23        28.27         5.33         2.43 
TCGA-HW-A5KK TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6WH TCGA-S9-A6WM TCGA-TM-A7C3 
       12.76        14.53         5.03        38.56        19.86        54.77 
TCGA-VM-A8CA 
       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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
       13.71        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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85        31.69        26.17 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76O 
       24.99        25.55        21.57        95.11        22.29        17.16 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
        7.50        44.42        38.89         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-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YN 
       29.13        93.21         3.65        12.43        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       75.02        15.32         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       41.33        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 
       28.34        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        21.53        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        18.64 
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 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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-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-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       85.55        84.99        31.10        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        31.59        18.71        20.48        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        31.36        43.04        43.20         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.49               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             54.77             211.17 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            16.180             21.815 
[1] "0.5 - 54.8 (16.2)"  "0.0 - 211.2 (21.8)"
[1] "hr=" "5"  
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    22  21
  20Q GAIN WILD-TYPE 206 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     22   21
  20Q GAIN WILD-TYPE  206  263
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               22                206
  MALE                 21                263
[1] 2 2
[1] FALSE
D36V4, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     9  31
  20Q GAIN WILD-TYPE 175 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      9   31
  20Q GAIN WILD-TYPE  175  262
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 9                175
  YES               31                262
[1] 2 2
[1] FALSE
D36V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20Q GAIN MUTATED            21                8                14
  20Q GAIN WILD-TYPE         173              121               175
D36V6, multiclass
                   clus
vv                  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASTROCYTOMA                     21                173
  OLIGOASTROCYTOMA                 8                121
  OLIGODENDROGLIOMA               14                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"
                    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                           2    39
  20Q GAIN WILD-TYPE                        19   433
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                       2                 19
  WHITE                                          39                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"
D36V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     1  39
  20Q GAIN WILD-TYPE  31 407
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1   39
  20Q GAIN WILD-TYPE   31  407
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 31
  NOT HISPANIC OR LATINO               39                407
[1] 2 2
[1] FALSE

Clustering(37) Variable = 21Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    14  10
  21Q GAIN WILD-TYPE 374 111
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                24                485 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                111 
$`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        24.43        33.96        20.98        11.41        41.13 
TCGA-E1-A7YQ TCGA-FG-5962 TCGA-FG-7634 TCGA-HT-7605 TCGA-HT-A5RA TCGA-HT-A74H 
       51.88        47.77        15.35         4.57        27.35         2.43 
TCGA-HT-A74L TCGA-QH-A6CV TCGA-QH-A6X9 TCGA-S9-A6WH TCGA-S9-A6WL TCGA-TM-A84H 
       11.05        14.53         1.91        38.56        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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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 
       63.88        46.06         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        23.21        17.46        13.71 
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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85        31.69 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 
       26.17        24.99        25.55        21.57        95.11        22.29 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76        17.16        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       95.57       130.78        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       15.32         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       41.33        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 
       28.34        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        21.53        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 
       18.64         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-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47        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-A5RB TCGA-HT-A5RC 
       26.04         0.13        20.22         0.07         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-A74J TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7486 
       17.52        17.65        10.52        15.35         0.10        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       14.53        16.34        16.73        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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       85.55        84.99        19.86        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       40.64        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       26.99        31.36        43.04        43.20        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        7.89        39.16        20.02        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 

  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 
             25.89              20.71 
[1] "1.2 - 211.2 (25.9)" "0.0 - 182.3 (20.7)"
[1] "hr=" "1.6"
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    13  11
  21Q GAIN WILD-TYPE 215 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     13   11
  21Q GAIN WILD-TYPE  215  273
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               13                215
  MALE                 11                273
[1] 2 2
[1] FALSE
D37V4, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     5  17
  21Q GAIN WILD-TYPE 179 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5   17
  21Q GAIN WILD-TYPE  179  276
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 5                179
  YES               17                276
[1] 2 2
[1] FALSE
D37V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  21Q GAIN MUTATED             9                5                10
  21Q GAIN WILD-TYPE         185              124               179
D37V6, multiclass
                   clus
vv                  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASTROCYTOMA                      9                185
  OLIGOASTROCYTOMA                 5                124
  OLIGODENDROGLIOMA               10                179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           1    22
  21Q GAIN WILD-TYPE                        20   450
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                       1                 20
  WHITE                                          22                450
[1] 4 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  24
  21Q GAIN WILD-TYPE  32 422
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   24
  21Q GAIN WILD-TYPE   32  422
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO               24                422
[1] 2 2
[1] FALSE

Clustering(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    19   4
  22Q GAIN WILD-TYPE 369 117
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                486 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                117 
$`22Q GAIN MUTATED`
TCGA-CS-6665 TCGA-CS-6668 TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-A7TI TCGA-E1-A7YQ 
       12.43        49.94        52.11         1.22        38.89        51.88 
TCGA-FG-5962 TCGA-HT-7468 TCGA-HT-8012 TCGA-P5-A737 TCGA-P5-A77X TCGA-QH-A6CZ 
       47.77         6.67         9.40        12.23         3.45         9.17 
TCGA-R8-A6ML TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A847 TCGA-S9-A6WM TCGA-TM-A84J 
       94.03        59.38        30.87        30.67        19.86        24.16 
TCGA-TQ-A7RI TCGA-TQ-A7RQ TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VV-A829 
        2.04        26.14        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        46.95         7.56        49.12         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 
       91.13        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 
       63.88        46.06         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        23.21        17.46        13.71 
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         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        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 
       33.27        29.85        31.69        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76        17.16        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       84.33        51.52        37.38         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       75.02        15.32         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        25.48        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        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        21.53 
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        18.64         5.72        27.52         0.10 
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-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24        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        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        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 
        7.99         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         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A77W 
       10.95         9.01        13.61         9.60         7.56        19.20 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        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-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-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6MO 
       16.50         5.03        11.08        12.99        88.83        32.65 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS 
        5.46         9.90        28.08         2.07        19.59        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        41.10        28.14        35.38        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       24.39        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       38.56        84.99        31.10        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        24.92        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
       15.98        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       30.05        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       43.04        43.20         7.89        39.16        20.02        23.47 
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 

  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 
             24.16              20.81 
[1] "0.1 - 94.0 (24.2)"  "0.0 - 211.2 (20.8)"
[1] "hr=" "1.2"
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    11  12
  22Q GAIN WILD-TYPE 217 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     11   12
  22Q GAIN WILD-TYPE  217  272
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               11                217
  MALE                 12                272
[1] 2 2
[1] FALSE
D38V4, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    12  10
  22Q GAIN WILD-TYPE 172 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     12   10
  22Q GAIN WILD-TYPE  172  283
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                12                172
  YES               10                283
[1] 2 2
[1] FALSE
D38V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  22Q GAIN MUTATED             3                4                16
  22Q GAIN WILD-TYPE         191              125               173
D38V6, multiclass
                   clus
vv                  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASTROCYTOMA                      3                191
  OLIGOASTROCYTOMA                 4                125
  OLIGODENDROGLIOMA               16                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"
                    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                           1    20
  22Q GAIN WILD-TYPE                        20   452
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                       1                 20
  WHITE                                          20                452
[1] 4 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     3  18
  22Q GAIN WILD-TYPE  29 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   18
  22Q GAIN WILD-TYPE   29  428
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 29
  NOT HISPANIC OR LATINO               18                428
[1] 2 2
[1] FALSE

Clustering(39) Variable = XP GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    17   4
  XP GAIN WILD-TYPE 371 117
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               21               488 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                4               117 
$`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        24.43        24.99        50.14 
TCGA-E1-A7YI TCGA-HT-7688 TCGA-HT-8013 TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7493 
        3.65        31.69        63.55        10.52         0.10        69.27 
TCGA-QH-A6CV TCGA-S9-A7QW TCGA-S9-A7QX TCGA-TM-A84H TCGA-TQ-A7RV TCGA-VM-A8C8 
       14.53        15.06        18.54        30.44        61.41        43.04 
TCGA-VM-A8CF TCGA-WY-A859 TCGA-WY-A85E 
       20.02        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        46.95        49.94        49.12         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        91.13 
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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       46.06         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        23.21        17.46        13.71        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         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       154.36        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        33.27        29.85        31.69        26.17        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76        17.16        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YJ 
       95.57       130.78        14.30        29.13        93.21        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ 
       12.43        16.18        21.30        23.90        75.02        51.88 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       15.32         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         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        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        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        21.53 
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        18.64         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-8015 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24         9.40         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-A74K 
       16.83        21.40        17.52        17.65         2.43        15.35 
TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
       11.05        56.58        13.45        41.49        45.60        68.32 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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         7.99         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         0.23 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
        2.04        20.68        28.37        27.16       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        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       36.69        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       33.93        26.99        31.36        43.20        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        39.16        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 
            69.27            211.17 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            24.43             20.76 
[1] "0.1 - 69.3 (24.4)"  "0.0 - 211.2 (20.8)"
[1] "hr=" "1.1"
D39V2, continuous
D39V3, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    13   8
  XP GAIN WILD-TYPE 215 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     13    8
  XP GAIN WILD-TYPE  215  276
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              13               215
  MALE                 8               276
[1] 2 2
[1] FALSE
D39V4, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     5  15
  XP GAIN WILD-TYPE 179 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      5   15
  XP GAIN WILD-TYPE  179  278
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                5               179
  YES              15               278
[1] 2 2
[1] FALSE
D39V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XP GAIN MUTATED            13                5                 3
  XP GAIN WILD-TYPE         181              124               186
D39V6, multiclass
                   clus
vv                  XP GAIN MUTATED XP GAIN WILD-TYPE
  ASTROCYTOMA                    13               181
  OLIGOASTROCYTOMA                5               124
  OLIGODENDROGLIOMA               3               186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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    19
  XP GAIN WILD-TYPE                        20   453
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                20
  WHITE                                         19               453
[1] 4 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     1  16
  XP GAIN WILD-TYPE  31 430
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1   16
  XP GAIN WILD-TYPE   31  430
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                31
  NOT HISPANIC OR LATINO              16               430
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    32   7
  XQ GAIN WILD-TYPE 356 114
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               39               470 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               114 
$`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-E1-A7YI 
       62.96        31.69        24.43        24.99       130.78         3.65 
TCGA-FG-A4MY TCGA-FG-A713 TCGA-HT-7476 TCGA-HT-7609 TCGA-HT-7688 TCGA-HT-7689 
       23.70        20.45         6.54        45.99        31.69        14.96 
TCGA-HT-7857 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8563 TCGA-HT-A74J TCGA-HT-A74O 
        0.23        31.43        63.55        28.27        10.52         0.10 
TCGA-QH-A65S TCGA-QH-A6CV TCGA-S9-A6TS TCGA-S9-A7IZ TCGA-S9-A7QX TCGA-TM-A84H 
        2.53        14.53        62.17        19.99        18.54        30.44 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RV TCGA-VM-A8CF TCGA-VV-A86M TCGA-WY-A858 
       40.41        44.09        61.41        20.02        16.01        43.96 
TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85E 
       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        46.95         7.56        49.94        49.12         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 
       91.13        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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       46.06         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        23.21        17.46        13.71        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         2.40        11.47       156.23       154.36        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        33.27        29.85        26.17 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76        17.16        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
      134.27        78.21        95.57        14.30        29.13        93.21 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       51.88        15.32         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         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        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        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-A60J TCGA-FG-A60K TCGA-FG-A60L 
       10.72        18.38        18.71        14.76        17.82        21.53 
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-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       48.69        18.64         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-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42        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-7610 
      122.47         4.57        17.29         3.16        22.06        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-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-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-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24         9.40         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-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-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-A74K TCGA-HT-A74L 
       21.40        17.52        17.65         2.43        15.35        11.05 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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         7.99         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         0.23 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        4.41        15.16        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-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        87.12        18.77        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       85.55        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       23.51        20.02         8.19         2.04        20.68        15.06 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       40.64        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       15.98         2.04        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       26.14        25.87        33.93        26.99        31.36        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       43.20        13.51         0.10         7.89        39.16        23.47 
TCGA-VV-A829 TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A85A 
       37.05        23.21         8.05        51.06        13.32        43.40 
TCGA-WY-A85C TCGA-WY-A85D 
       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 
            24.99             20.68 
[1] "0.1 - 130.8 (25.0)" "0.0 - 211.2 (20.7)"
[1] "hr=" "1.5"
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    26  13
  XQ GAIN WILD-TYPE 202 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     26   13
  XQ GAIN WILD-TYPE  202  271
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              26               202
  MALE                13               271
[1] 2 2
[1] FALSE
D40V4, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    11  26
  XQ GAIN WILD-TYPE 173 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     11   26
  XQ GAIN WILD-TYPE  173  267
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               11               173
  YES              26               267
[1] 2 2
[1] FALSE
D40V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XQ GAIN MUTATED            18               15                 6
  XQ GAIN WILD-TYPE         176              114               183
D40V6, multiclass
                   clus
vv                  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASTROCYTOMA                    18               176
  OLIGOASTROCYTOMA               15               114
  OLIGODENDROGLIOMA               6               183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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    35
  XQ GAIN WILD-TYPE                        19   437
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                19
  WHITE                                         35               437
[1] 4 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     6  28
  XQ GAIN WILD-TYPE  26 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6   28
  XQ GAIN WILD-TYPE   26  418
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                26
  NOT HISPANIC OR LATINO              28               418
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   156  26
  1P LOSS WILD-TYPE 232  95
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              182               327 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               26                95 
$`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        49.94         6.61        75.25 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       91.13        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 
       23.21        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       154.36       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 
       25.55        21.57        95.11        22.29        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-E1-A7YS TCGA-E1-A7YY TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 
       15.32       146.14        39.48         0.23        47.77        52.21 
TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       15.35        22.55        20.61        14.24        16.01        20.09 
TCGA-FG-8189 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 
       22.52        17.82        15.02        16.44        36.66        20.45 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7481 
        0.10         6.67         0.13        24.26        75.19        95.93 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 
        4.57         3.16        22.06         0.23        14.27        16.24 
TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 
       44.68         0.10         2.96         6.90        14.53        39.09 
TCGA-HT-7857 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 
        0.23        37.15         0.33         0.13        35.47         1.64 
TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-A4DV TCGA-HT-A5R9 
        9.40         6.25         5.56        29.59        26.04         0.07 
TCGA-HT-A615 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 
       16.93        21.40        17.65        15.35        11.05        56.58 
TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 
       13.45        68.32        35.44         6.18        10.55        42.77 
TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A72Z TCGA-P5-A730 
       14.40         7.99         4.11         0.76        11.64        10.95 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65V TCGA-QH-A65X 
       12.23        19.20         3.45         4.41        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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD 
       28.14        35.38        29.85        32.61       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP 
      135.22        38.56        84.99        31.10        26.47        18.64 
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        20.68        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O 
       27.16       169.84        49.32        40.64        24.79        33.24 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RN TCGA-TQ-A7RO 
       18.61        14.93        19.69         2.04        33.73        31.20 
TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 
       26.14        33.93        13.51         0.10        39.16        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 
       46.95         7.56        49.12       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 
       63.88        46.06        42.05        27.81        17.19        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       13.71        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         2.40        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        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 
       31.69        24.43        26.17        24.99        33.96        20.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       11.41        26.76        17.16       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       37.38         7.50        38.89         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       41.13        79.99        57.93        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       51.88         0.76        32.45        36.82        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 
      145.05        32.35         0.20        25.48        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7643 
       14.93        42.54        41.33        18.44        17.88        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       28.34        13.68        14.96        32.61        38.27        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        21.53        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        18.64         5.72        27.52 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       11.54        40.11         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        6.54         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-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 
       31.69        14.96         0.10         0.10        17.52        39.48 
TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 
       19.23        50.63         0.49        23.61         3.68         5.33 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 
        3.72        11.28        31.43        16.24        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01        12.23         0.10         0.46         2.50 
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-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13        20.22        27.35         0.10         5.33         2.70 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74H TCGA-HT-A74J 
        1.81        16.14        16.83        17.52         2.43        10.52 
TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 
        0.10        41.49        45.60        69.27        39.75        40.01 
TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 
       42.54        12.76        20.81        20.71        19.00        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 
        0.23         6.71         2.37         2.30         5.88         7.63 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A731 TCGA-P5-A733 
        1.28         0.23        10.42        13.25         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A780 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A6CS 
        9.60         7.56         2.37        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        36.82        24.39        25.81        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WQ 
       95.93         5.85        85.55        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        26.93        19.99        20.02        15.06        18.54 
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 
       20.48        54.77        48.33        34.78        65.39        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-A7RF TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       25.38        23.80        21.37        15.98        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RP TCGA-TQ-A7RR TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       36.69        30.05        25.87        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A86M 
       43.04        43.20         7.89        20.02        23.47        16.01 
TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        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 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 
           22.175            20.220 
[1] "0.1 - 182.3 (22.2)" "0.0 - 211.2 (20.2)"
[1] "hr=" "2.3"
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    83 101
  1P LOSS WILD-TYPE 145 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     83  101
  1P LOSS WILD-TYPE  145  183
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              83               145
  MALE               101               183
[1] 2 2
[1] FALSE
D41V4, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    94  77
  1P LOSS WILD-TYPE  90 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     94   77
  1P LOSS WILD-TYPE   90  216
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               94                90
  YES              77               216
[1] 2 2
[1] FALSE
D41V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1P LOSS MUTATED            10               39               135
  1P LOSS WILD-TYPE         184               90                54
D41V6, multiclass
                   clus
vv                  1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASTROCYTOMA                    10               184
  OLIGOASTROCYTOMA               39                90
  OLIGODENDROGLIOMA             135                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           6   167
  1P LOSS WILD-TYPE                        15   305
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                      6                15
  WHITE                                        167               305
[1] 4 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    13 161
  1P LOSS WILD-TYPE  19 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     13  161
  1P LOSS WILD-TYPE   19  285
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                  13                19
  NOT HISPANIC OR LATINO             161               285
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    18   7
  1Q LOSS WILD-TYPE 370 114
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               484 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               114 
$`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        31.69        44.42       130.78 
TCGA-E1-A7YY TCGA-FG-5962 TCGA-FG-8185 TCGA-HT-7477 TCGA-HT-7857 TCGA-HT-8113 
      146.14        47.77        14.24        24.26         0.23        29.59 
TCGA-P5-A5F4 TCGA-QH-A65S TCGA-QH-A65Z TCGA-QH-A6CV TCGA-RY-A83Y TCGA-S9-A6WI 
        0.76         2.53        14.04        14.53         5.46        84.99 
TCGA-S9-A7R1 
      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        46.95         7.56        49.94        49.12 
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        91.13        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        63.88 
TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       46.06        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 
       23.21        17.46        13.71        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 
        2.40        11.47        62.96       156.23       154.36        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        33.27        29.85        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76        17.16        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TI TCGA-DU-A7TJ 
       84.33        51.52        37.38         7.50        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       78.21        95.57        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z2 
       51.88        15.32         0.76        32.45        36.82        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       20.09        28.34        13.68        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        21.53        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 
       18.64         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-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         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-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-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-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 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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         7.99         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         5.88         7.63         1.28         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW 
       15.16        12.62        15.85        19.33        14.83        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-A83Z 
       88.83        94.03        32.65        59.38        30.87         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        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       27.16        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        20.48        54.77        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  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 
            24.26             20.81 
[1] "0.2 - 169.8 (24.3)" "0.0 - 211.2 (20.8)"
[1] "hr=" "1.3"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    12  13
  1Q LOSS WILD-TYPE 216 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     12   13
  1Q LOSS WILD-TYPE  216  271
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              12               216
  MALE                13               271
[1] 2 2
[1] FALSE
D42V4, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9  14
  1Q LOSS WILD-TYPE 175 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   14
  1Q LOSS WILD-TYPE  175  279
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                9               175
  YES              14               279
[1] 2 2
[1] FALSE
D42V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1Q LOSS MUTATED             4                4                17
  1Q LOSS WILD-TYPE         190              125               172
D42V6, multiclass
                   clus
vv                  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASTROCYTOMA                     4               190
  OLIGOASTROCYTOMA                4               125
  OLIGODENDROGLIOMA              17               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"
                   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    21
  1Q LOSS WILD-TYPE                        19   451
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                19
  WHITE                                         21               451
[1] 4 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  23
  1Q LOSS WILD-TYPE  31 423
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   23
  1Q LOSS WILD-TYPE   31  423
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                31
  NOT HISPANIC OR LATINO              23               423
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    14   7
  2P LOSS WILD-TYPE 374 114
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               21               488 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7               114 
$`2P LOSS MUTATED`
TCGA-CS-6186 TCGA-CS-6666 TCGA-DH-5142 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-A7T6 
       17.69        46.95        63.88        14.99       117.40        17.98 
TCGA-E1-A7YH TCGA-E1-A7YK TCGA-FG-A6J3 TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7690 
       93.21        12.43        22.26        11.54        24.26         0.10 
TCGA-HT-7692 TCGA-HT-A5R7 TCGA-HT-A61B TCGA-HW-7493 TCGA-P5-A5F6 TCGA-P5-A733 
        2.96        20.22        17.52        69.27         1.28        13.61 
TCGA-QH-A6CW TCGA-S9-A89V TCGA-VM-A8C8 
       13.61        18.71        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        49.94        49.12         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 
       91.13        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 
       46.06         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        23.21        17.46        13.71        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         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       154.36       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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       26.76        17.16        21.30       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ 
       95.57       130.78        14.30        29.13         3.65        19.46 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS 
       16.18        21.30        23.90        75.02        51.88        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
        0.76        32.45        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         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        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        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        21.53        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-7470 
       18.64         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-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-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-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        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       45.60        68.32        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
        6.18        10.55        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         7.99 
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 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.83        14.53        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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
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 
       20.48        54.77        48.33        49.32        34.78        65.39 
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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       14.93        23.80        21.37        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       40.41        44.09        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       26.14        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF 
       43.20        13.51         0.10         7.89        39.16        20.02 
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 

  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 
           17.980            21.155 
[1] "0.1 - 117.4 (18.0)" "0.0 - 211.2 (21.2)"
[1] "hr=" "1.5"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     8  13
  2P LOSS WILD-TYPE 220 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      8   13
  2P LOSS WILD-TYPE  220  271
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               8               220
  MALE                13               271
[1] 2 2
[1] FALSE
D43V4, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2  17
  2P LOSS WILD-TYPE 182 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   17
  2P LOSS WILD-TYPE  182  276
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                2               182
  YES              17               276
[1] 2 2
[1] FALSE
D43V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2P LOSS MUTATED            12                4                 5
  2P LOSS WILD-TYPE         182              125               184
D43V6, multiclass
                   clus
vv                  2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASTROCYTOMA                    12               182
  OLIGOASTROCYTOMA                4               125
  OLIGODENDROGLIOMA               5               184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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    21
  2P LOSS WILD-TYPE                        21   451
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                21
  WHITE                                         21               451
[1] 4 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  20
  2P LOSS WILD-TYPE  32 426
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   20
  2P LOSS WILD-TYPE   32  426
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO              20               426
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    13   5
  2Q LOSS WILD-TYPE 375 116
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               491 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5               116 
$`2Q LOSS MUTATED`
TCGA-CS-6666 TCGA-DB-5277 TCGA-DH-5142 TCGA-DH-A66B TCGA-DU-6408 TCGA-DU-A7T6 
       46.95        50.86        63.88        42.05       114.08        17.98 
TCGA-E1-A7YH TCGA-E1-A7YK TCGA-FG-A6J3 TCGA-HT-7477 TCGA-HT-7690 TCGA-HT-7692 
       93.21        12.43        22.26        24.26         0.10         2.96 
TCGA-HT-A618 TCGA-HT-A61B TCGA-HW-7493 TCGA-P5-A5F6 TCGA-P5-A733 TCGA-QH-A6CW 
       16.83        17.52        69.27         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        49.94        49.12 
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 
       91.13        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 
       46.06         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        23.21        17.46        13.71        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         2.40        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      154.36        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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       26.76        17.16        21.30       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ 
       95.57       130.78        14.30        29.13         3.65        19.46 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS 
       16.18        21.30        23.90        75.02        51.88        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
        0.76        32.45        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         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        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        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        21.53        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 
       18.64         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-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         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-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-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-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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       41.49        45.60        68.32        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        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 
        7.99         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        0.76         0.23        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
        9.01         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        19.33        14.83        14.53        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 
       41.10        28.14        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       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        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       26.99        31.36        43.04        43.20        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        7.89        39.16        20.02        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 

  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 
            20.12             20.81 
[1] "0.1 - 114.1 (20.1)" "0.0 - 211.2 (20.8)"
[1] "hr=" "1.1"
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7  11
  2Q LOSS WILD-TYPE 221 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7   11
  2Q LOSS WILD-TYPE  221  273
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               7               221
  MALE                11               273
[1] 2 2
[1] FALSE
D44V4, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     3  13
  2Q LOSS WILD-TYPE 181 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3   13
  2Q LOSS WILD-TYPE  181  280
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                3               181
  YES              13               280
[1] 2 2
[1] FALSE
D44V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2Q LOSS MUTATED            12                3                 3
  2Q LOSS WILD-TYPE         182              126               186
D44V6, multiclass
                   clus
vv                  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASTROCYTOMA                    12               182
  OLIGOASTROCYTOMA                3               126
  OLIGODENDROGLIOMA               3               186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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    18
  2Q LOSS WILD-TYPE                        21   454
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                21
  WHITE                                         18               454
[1] 4 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  18
  2Q LOSS WILD-TYPE  32 428
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   18
  2Q LOSS WILD-TYPE   32  428
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO              18               428
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    18  11
  3P LOSS WILD-TYPE 370 110
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               29               480 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               11               110 
$`3P LOSS MUTATED`
TCGA-CS-6666 TCGA-DB-5277 TCGA-DH-A66D TCGA-DU-6396 TCGA-DU-7300 TCGA-DU-A5TU 
       46.95        50.86        27.81        75.16        62.01        26.17 
TCGA-DU-A76R TCGA-DU-A7TA TCGA-E1-A7YJ TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-E1-A7YW 
       21.30        84.33        19.46        51.88        32.45        36.82 
TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7690 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A5RA 
       11.54        24.26         0.10         0.23        15.72        27.35 
TCGA-HT-A619 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-P5-A77W TCGA-P5-A780 TCGA-S9-A89V 
       21.40        19.00         1.28        19.20         2.37        18.71 
TCGA-TM-A84B TCGA-TM-A84J TCGA-TQ-A7RH TCGA-VM-A8C8 TCGA-VV-A829 
       24.92        24.16        15.98        43.04        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        49.94        49.12 
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 
       91.13        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 
       63.88        46.06         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        23.21        17.46        13.71        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         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       29.85        31.69        24.43        24.99        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       21.57        95.11        20.98        22.29        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.16        17.98       139.04        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YL 
       14.30        29.13        93.21         3.65        12.43        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YY 
       21.30        23.90        75.02        15.32         0.76       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         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        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        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 
       21.53        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        18.64         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-7692 TCGA-HT-7693 TCGA-HT-7694 
       31.69        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-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-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13        20.22         0.07         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C 
       16.93         1.81        16.14        16.83        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        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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         7.99         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-A72Z 
        7.63         0.76         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        3.45         4.41        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-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       14.93        23.80        21.37        19.69         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 
       25.87        33.93        61.41        26.99        31.36        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        23.47 
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 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.10              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            84.33            211.17 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            24.26             20.68 
[1] "0.1 - 84.3 (24.3)"  "0.0 - 211.2 (20.7)"
[1] "hr=" "1.9"
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    11  19
  3P LOSS WILD-TYPE 217 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     11   19
  3P LOSS WILD-TYPE  217  265
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              11               217
  MALE                19               265
[1] 2 2
[1] FALSE
D45V4, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     8  21
  3P LOSS WILD-TYPE 176 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      8   21
  3P LOSS WILD-TYPE  176  272
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                8               176
  YES              21               272
[1] 2 2
[1] FALSE
D45V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3P LOSS MUTATED            12                8                10
  3P LOSS WILD-TYPE         182              121               179
D45V6, multiclass
                   clus
vv                  3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASTROCYTOMA                    12               182
  OLIGOASTROCYTOMA                8               121
  OLIGODENDROGLIOMA              10               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           2    27
  3P LOSS WILD-TYPE                        19   445
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                      2                19
  WHITE                                         27               445
[1] 4 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  26
  3P LOSS WILD-TYPE  29 420
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3   26
  3P LOSS WILD-TYPE   29  420
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                29
  NOT HISPANIC OR LATINO              26               420
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    15  13
  3Q LOSS WILD-TYPE 373 108
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               28               481 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13               108 
$`3Q LOSS MUTATED`
TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5281 TCGA-DU-6396 TCGA-DU-7007 TCGA-DU-7014 
       46.95        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        26.17        21.30        50.14 
TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-HT-7469 TCGA-HT-7472 TCGA-HT-7477 TCGA-HT-8111 
       51.88        32.45        11.54         0.03        24.26         0.23 
TCGA-HT-8564 TCGA-HT-A619 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-P5-A77W TCGA-P5-A780 
       15.72        21.40        19.00         1.28        19.20         2.37 
TCGA-S9-A6TV TCGA-TM-A84B TCGA-TM-A84J TCGA-VM-A8C8 
       18.77        24.92        24.16        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        49.94        49.12 
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 
       91.13        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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       46.06         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        23.21        17.46        13.71        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         2.40        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      154.36        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        33.27        29.85        31.69        24.43        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76        17.16        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       95.57       130.78        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       15.32         0.76        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         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        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        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        21.53        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        18.64         5.72        27.52         0.10         6.67 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       40.11         0.13        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-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-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       34.19        28.27         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-A61B TCGA-HT-A61C TCGA-HT-A74H 
        1.81        16.14        16.83        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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        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 
        7.99         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        0.76         0.23        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77X 
        9.01        13.61         9.60         7.56        12.23         3.45 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        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-A6TW 
        2.07        19.59        30.67        62.17        87.12        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
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        20.48        54.77        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 
       25.87        33.93        61.41        26.99        31.36        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        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 
            24.21             20.68 
[1] "0.0 - 117.4 (24.2)" "0.1 - 211.2 (20.7)"
[1] "hr=" "1.9"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    11  17
  3Q LOSS WILD-TYPE 217 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     11   17
  3Q LOSS WILD-TYPE  217  267
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              11               217
  MALE                17               267
[1] 2 2
[1] FALSE
D46V4, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     7  19
  3Q LOSS WILD-TYPE 177 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      7   19
  3Q LOSS WILD-TYPE  177  274
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                7               177
  YES              19               274
[1] 2 2
[1] FALSE
D46V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3Q LOSS MUTATED            10                7                11
  3Q LOSS WILD-TYPE         184              122               178
D46V6, multiclass
                   clus
vv                  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASTROCYTOMA                    10               184
  OLIGOASTROCYTOMA                7               122
  OLIGODENDROGLIOMA              11               178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           2    25
  3Q LOSS WILD-TYPE                        19   447
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                      2                19
  WHITE                                         25               447
[1] 4 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  25
  3Q LOSS WILD-TYPE  30 421
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   25
  3Q LOSS WILD-TYPE   30  421
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                30
  NOT HISPANIC OR LATINO              25               421
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    55  16
  4P LOSS WILD-TYPE 333 105
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               71               438 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               16               105 
$`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        17.46        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        21.57        22.29        21.30       139.04 
TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5311 TCGA-E1-A7YS 
       84.33        50.14        67.46        41.13       134.27        15.32 
TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-A60J 
        0.23        47.77        52.21        17.88        22.55        14.76 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7475 
       15.02        16.44         0.10         6.67         0.13        17.42 
TCGA-HT-7480 TCGA-HT-7677 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-8105 TCGA-HT-A5R9 
       75.19        16.24        31.69         2.96         6.25         0.07 
TCGA-HT-A619 TCGA-HT-A74K TCGA-HW-7487 TCGA-HW-7491 TCGA-IK-8125 TCGA-P5-A5EV 
       21.40        15.35        13.45        68.32        42.77         0.23 
TCGA-P5-A735 TCGA-P5-A737 TCGA-P5-A77W TCGA-S9-A6TW TCGA-S9-A6UB TCGA-S9-A6WD 
        9.60        12.23        19.20        41.10       123.65        75.25 
TCGA-S9-A6WL TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-TM-A7C5 TCGA-TM-A84T TCGA-TQ-A7RM 
       31.10        23.51        19.99        49.32        23.80        36.69 
TCGA-TQ-A7RO TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-WH-A86K 
       31.20        25.87        33.93        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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-5278 
       49.12         6.61       122.73        81.96        72.92        91.13 
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 
       63.88        46.06         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        23.21        13.71        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         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       154.36       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        33.27        29.85        31.69        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 
       26.17        24.99        33.96        25.55        95.11        20.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC 
       11.41        26.76        17.16        17.98        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5305 TCGA-E1-5307 
        7.50        44.42        38.89         0.56        79.99        57.93 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       75.02        51.88         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O4 
       13.08        73.48       145.05        32.35        39.48         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        42.54        41.33 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       18.44        15.35        20.61        20.09        28.34        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-A60K 
       38.27        10.72        18.38        18.71        23.70        17.82 
TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       21.53        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 
       20.45        18.64         5.72        27.52        11.54        40.11 
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-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-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-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-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13        20.22        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C 
       16.93         1.81        16.14        16.83        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7489 
        2.43        10.52        11.05         0.10        56.58        41.49 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       45.60        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
        6.18        10.55        12.76        20.81        20.71        19.00 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40        14.40         6.71         7.99         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         0.23 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A736 TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
        7.56         3.45         2.37         4.41        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-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       62.17        87.12        18.77        28.14        35.38        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       24.39        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
       95.93         5.85       135.22        85.55        38.56        84.99 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
        7.92        26.93        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        18.54        28.37        27.16       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        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       54.77        48.33        34.78        65.39        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-TQ-A7RF 
       24.79        33.24        25.38        18.61        14.93        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN 
       19.69        15.98         2.04        40.41        44.09        33.73 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       30.05        26.14        61.41        31.36        43.04        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        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 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.07              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           139.04            211.17 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           21.570            20.695 
[1] "0.1 - 139.0 (21.6)" "0.0 - 211.2 (20.7)"
[1] "hr=" "1.1"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    24  47
  4P LOSS WILD-TYPE 204 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     24   47
  4P LOSS WILD-TYPE  204  237
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              24               204
  MALE                47               237
[1] 2 2
[1] FALSE
D47V4, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    25  39
  4P LOSS WILD-TYPE 159 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     25   39
  4P LOSS WILD-TYPE  159  254
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               25               159
  YES              39               254
[1] 2 2
[1] FALSE
D47V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4P LOSS MUTATED            13               19                39
  4P LOSS WILD-TYPE         181              110               150
D47V6, multiclass
                   clus
vv                  4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASTROCYTOMA                    13               181
  OLIGOASTROCYTOMA               19               110
  OLIGODENDROGLIOMA              39               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"
                   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                           2    66
  4P LOSS WILD-TYPE                        19   406
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                      2                19
  WHITE                                         66               406
[1] 4 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     5  64
  4P LOSS WILD-TYPE  27 382
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5   64
  4P LOSS WILD-TYPE   27  382
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                27
  NOT HISPANIC OR LATINO              64               382
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    73  19
  4Q LOSS WILD-TYPE 315 102
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               92               417 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               19               102 
$`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        31.69        21.57        22.29        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5311 
      139.04        84.33        50.14        67.46        41.13       134.27 
TCGA-E1-A7YK TCGA-E1-A7YS TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5963 
       12.43        15.32        39.48         0.23        47.77        25.48 
TCGA-FG-5964 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 
       52.21        17.88        22.55        14.76        15.02        16.44 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7677 TCGA-HT-7688 
        0.10         6.67         0.13        75.19        16.24        31.69 
TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-8105 TCGA-HT-A5R9 TCGA-HT-A619 TCGA-HT-A74K 
        2.96        39.09         6.25         0.07        21.40        15.35 
TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7493 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A735 
       13.45        68.32        69.27        42.77         0.23         9.60 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A780 TCGA-QH-A6X4 TCGA-QH-A6XA TCGA-S9-A6TW 
       12.23        19.20         2.37        14.53        16.50        41.10 
TCGA-S9-A6WD TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ 
       75.25        31.10        18.64         7.92        23.51        19.99 
TCGA-S9-A7J0 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A84R TCGA-TM-A84T TCGA-TQ-A7RM 
       20.02        48.33        49.32        18.61        23.80        36.69 
TCGA-TQ-A7RO TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-WH-A86K TCGA-WY-A859 
       31.20        25.87        33.93        26.99        13.32        39.88 
TCGA-WY-A85A TCGA-WY-A85E 
       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        46.95         7.56        49.94        49.12 
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        91.13        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        63.88        46.06 
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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        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         2.40        11.47        62.96       154.36 
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        33.27        29.85        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K 
       24.99        33.96        25.55        95.11        20.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       26.76        17.16        17.98        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 
       44.42        38.89         0.56        79.99        57.93        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       95.57       130.78        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ 
       19.46        16.18        21.30        23.90        75.02        51.88 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
        0.76        32.45        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
      145.05        32.35         0.20        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 
       42.54        41.33        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 
       28.34        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        21.53        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        18.64         5.72        27.52 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       11.54        40.11         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-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-7680 TCGA-HT-7681 
       57.60         0.23        14.27         0.16         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-7857 
       17.52         6.90        14.53        39.48        19.23         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-7495 TCGA-HW-8319 TCGA-HW-8320 
       56.58        41.49        45.60        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       19.00        14.40        14.40         6.71         7.99         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 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A736 TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       13.61         7.56         3.45         4.41        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        28.14        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM 
      123.65       135.22        85.55        38.56        84.99        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7J1 
       26.47        18.61        14.07        36.13        26.93         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
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        20.48        54.77        34.78        65.39        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-A7RF 
       40.83        24.79        33.24        25.38        14.93        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN 
       19.69        15.98         2.04        40.41        44.09        33.73 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       30.05        26.14        61.41        31.36        43.04        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        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-A85B TCGA-WY-A85C TCGA-WY-A85D 
       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 
            23.03             20.48 
[1] "0.1 - 156.2 (23.0)" "0.0 - 211.2 (20.5)"
[1] "hr=" "1.3"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    35  57
  4Q LOSS WILD-TYPE 193 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     35   57
  4Q LOSS WILD-TYPE  193  227
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              35               193
  MALE                57               227
[1] 2 2
[1] FALSE
D48V4, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    34  50
  4Q LOSS WILD-TYPE 150 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     34   50
  4Q LOSS WILD-TYPE  150  243
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               34               150
  YES              50               243
[1] 2 2
[1] FALSE
D48V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4Q LOSS MUTATED            23               23                46
  4Q LOSS WILD-TYPE         171              106               143
D48V6, multiclass
                   clus
vv                  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASTROCYTOMA                    23               171
  OLIGOASTROCYTOMA               23               106
  OLIGODENDROGLIOMA              46               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"
                   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                           3    86
  4Q LOSS WILD-TYPE                        18   386
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                      3                18
  WHITE                                         86               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"
D48V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     5  81
  4Q LOSS WILD-TYPE  27 365
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5   81
  4Q LOSS WILD-TYPE   27  365
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                27
  NOT HISPANIC OR LATINO              81               365
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    26   8
  5P LOSS WILD-TYPE 362 113
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               475 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8               113 
$`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-E1-A7Z4 
       62.96        41.98        19.13        17.98        50.14       145.05 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-A6J3 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7688 
       36.82        14.93        22.26         3.75        17.42        31.69 
TCGA-HT-7884 TCGA-HT-8106 TCGA-HT-A614 TCGA-HT-A61B TCGA-P5-A72W TCGA-RY-A83Z 
       11.28         0.10         2.70        17.52        10.42         9.90 
TCGA-S9-A6WM TCGA-S9-A7R7 TCGA-TM-A84I TCGA-WY-A859 
       19.86        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        46.95         7.56        49.94        49.12 
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        91.13        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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A7UR 
       46.06         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 
       23.21        17.46        13.71        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         2.40        11.47       156.23       154.36        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        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
       22.29        11.41        26.76        17.16        21.30       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       75.02        51.88        15.32         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      146.14        13.08        73.48        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6690 
        0.20        47.77        25.48        52.21        18.77        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        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        21.53        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 
       18.64         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7477 
       40.11         0.13         0.03        16.54         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-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-8107 TCGA-HT-8108 
       37.87        33.01        12.23         6.25         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-A615 TCGA-HT-A616 TCGA-HT-A617 
       27.35         0.10         5.33        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        56.58        13.45        41.49        45.60 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       68.32        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
        6.18        10.55        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         7.99 
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-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        1.28         0.23        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        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-A840 
       94.03        32.65        59.38        30.87         5.46        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 
       41.10        28.14        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-S9-A89V 
      169.84        10.39        99.06        30.05        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       20.48        54.77        48.33        49.32        34.78        65.39 
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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       25.87        33.93        61.41        26.99        31.36        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF 
       43.20        13.51         0.10         7.89        39.16        20.02 
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-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       13.32        43.96        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.10              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           145.05            211.17 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           25.035            20.810 
[1] "0.1 - 145.1 (25.0)" "0.0 - 211.2 (20.8)"
[1] "hr=" "1.2"
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    14  20
  5P LOSS WILD-TYPE 214 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     14   20
  5P LOSS WILD-TYPE  214  264
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              14               214
  MALE                20               264
[1] 2 2
[1] FALSE
D49V4, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5  26
  5P LOSS WILD-TYPE 179 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5   26
  5P LOSS WILD-TYPE  179  267
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                5               179
  YES              26               267
[1] 2 2
[1] FALSE
D49V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5P LOSS MUTATED            18               11                 5
  5P LOSS WILD-TYPE         176              118               184
D49V6, multiclass
                   clus
vv                  5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASTROCYTOMA                    18               176
  OLIGOASTROCYTOMA               11               118
  OLIGODENDROGLIOMA               5               184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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    34
  5P LOSS WILD-TYPE                        21   438
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                21
  WHITE                                         34               438
[1] 4 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  32
  5P LOSS WILD-TYPE  32 414
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   32
  5P LOSS WILD-TYPE   32  414
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO              32               414
[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 367 109
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               476 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               12               109 
$`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        46.95         7.56        49.94        49.12 
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        91.13 
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        63.88        46.06         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        23.21        17.46        13.71        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         2.40        11.47       156.23       154.36       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        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
       22.29        11.41        26.76        17.16        21.30       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
        0.56        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       95.57       130.78        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       51.88        15.32         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         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        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        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 
       21.53        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        18.64         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-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-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-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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        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 
        7.99         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        0.76         1.28         0.23        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        3.45         2.37         4.41        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        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       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        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
        8.05        51.06        43.96        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       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 
           19.960            20.895 
[1] "0.1 - 114.1 (20.0)" "0.0 - 211.2 (20.9)"
[1] "hr=" "1.5"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    17  16
  5Q LOSS WILD-TYPE 211 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     17   16
  5Q LOSS WILD-TYPE  211  268
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              17               211
  MALE                16               268
[1] 2 2
[1] FALSE
D50V4, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     4  26
  5Q LOSS WILD-TYPE 180 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4   26
  5Q LOSS WILD-TYPE  180  267
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                4               180
  YES              26               267
[1] 2 2
[1] FALSE
D50V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5Q LOSS MUTATED            20                6                 7
  5Q LOSS WILD-TYPE         174              123               182
D50V6, multiclass
                   clus
vv                  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASTROCYTOMA                    20               174
  OLIGOASTROCYTOMA                6               123
  OLIGODENDROGLIOMA               7               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                        21   439
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                21
  WHITE                                         33               439
[1] 4 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  31 415
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   31
  5Q LOSS WILD-TYPE   31  415
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                31
  NOT HISPANIC OR LATINO              31               415
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    17  13
  6P LOSS WILD-TYPE 371 108
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               30               479 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               13               108 
$`6P LOSS MUTATED`
TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64O 
        6.38        46.95        50.86        33.57        31.63        25.48 
TCGA-DH-A669 TCGA-DU-6400 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-A7T6 TCGA-E1-A7YQ 
       30.21         1.22         5.10        23.74        17.98        51.88 
TCGA-E1-A7YS TCGA-FG-5963 TCGA-FG-8191 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-8564 
       15.32        25.48        32.61         2.96        19.23        15.72 
TCGA-HT-A4DS TCGA-HT-A617 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A780 TCGA-QH-A6CS 
        0.23        16.14         0.76         1.28         2.37        19.33 
TCGA-QH-A6CX TCGA-S9-A6TZ TCGA-TM-A7CF TCGA-TQ-A7RF TCGA-VM-A8C8 TCGA-VM-A8CD 
       12.23        36.82        65.39        21.37        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        49.94        49.12         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        91.13 
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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        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         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       154.36        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 
       33.27        29.85        31.69        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76        17.16        21.30       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       75.02         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       47.77        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       14.96        22.52        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        21.53        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 
       18.64         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-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         0.10        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        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-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
        1.81        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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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         7.99         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        7.63         0.23        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        3.45         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.04        14.83        14.53        13.61         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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.14        35.38        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       26.93        23.51        19.99        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       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-A84B 
       20.48        54.77        48.33        49.32        34.78        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-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       23.80        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       36.69        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CA 
       33.93        61.41        26.99        31.36        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10        39.16        20.02        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 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.23              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            65.39            211.17 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            19.28             20.98 
[1] "0.2 - 65.4 (19.3)"  "0.0 - 211.2 (21.0)"
[1] "hr=" "3.1"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    15  15
  6P LOSS WILD-TYPE 213 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     15   15
  6P LOSS WILD-TYPE  213  269
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              15               213
  MALE                15               269
[1] 2 2
[1] FALSE
D51V4, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  20
  6P LOSS WILD-TYPE 179 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   20
  6P LOSS WILD-TYPE  179  273
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                5               179
  YES              20               273
[1] 2 2
[1] FALSE
D51V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6P LOSS MUTATED            15                4                11
  6P LOSS WILD-TYPE         179              125               178
D51V6, multiclass
                   clus
vv                  6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASTROCYTOMA                    15               179
  OLIGOASTROCYTOMA                4               125
  OLIGODENDROGLIOMA              11               178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           2    27
  6P LOSS WILD-TYPE                        19   445
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                      2                19
  WHITE                                         27               445
[1] 4 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  26
  6P LOSS WILD-TYPE  31 420
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   26
  6P LOSS WILD-TYPE   31  420
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                31
  NOT HISPANIC OR LATINO              26               420
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    41  20
  6Q LOSS WILD-TYPE 347 101
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               61               448 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               20               101 
$`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        46.95        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         2.40         6.54        18.94         5.10 
TCGA-DU-8161 TCGA-DU-A7T6 TCGA-DU-A7TC TCGA-E1-5307 TCGA-E1-A7YK TCGA-E1-A7YQ 
       23.74        17.98        37.38        57.93        12.43        51.88 
TCGA-E1-A7YS TCGA-E1-A7Z2 TCGA-FG-5963 TCGA-FG-7636 TCGA-FG-8191 TCGA-FG-A6J3 
       15.32        13.08        25.48        17.88        32.61        22.26 
TCGA-HT-7475 TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 
       17.42        17.29        31.69        14.96         2.96        19.23 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RB TCGA-HT-A617 TCGA-HT-A619 TCGA-HW-A5KK 
       15.72         0.23         0.10        16.14        21.40        12.76 
TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W 
        0.23         2.30         7.63         0.76         1.28        10.42 
TCGA-P5-A780 TCGA-QH-A6CS TCGA-QH-A6CX TCGA-QH-A870 TCGA-S9-A6TZ TCGA-S9-A7R8 
        2.37        19.33        12.23        12.99        36.82        31.59 
TCGA-TM-A7CF TCGA-TM-A84Q TCGA-TQ-A7RF TCGA-VM-A8C8 TCGA-VM-A8CD TCGA-VM-A8CF 
       65.39        25.38        21.37        43.04         7.89        20.02 
TCGA-WY-A85B 
       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        49.94        49.12         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        91.13 
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        63.88        46.06         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        23.21        17.46        13.71        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       154.36        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        33.27        29.85        31.69 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       24.43        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       95.11        20.98        22.29        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG 
       21.30       139.04        84.33        51.52         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       38.89         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE 
      134.27        78.21        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
       93.21         3.65        19.46        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 
       75.02         0.76        32.45        36.82       146.14        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         0.23         0.20        47.77 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       52.21        36.82        18.77        14.93        42.54        41.33 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       18.44        15.35        22.55        20.61        20.09        28.34 
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-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        21.53        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        18.64         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-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75         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-7607 TCGA-HT-7608 
       29.85        23.18       122.47         4.57         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-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-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-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       34.19        28.27        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 
       27.35         5.33         2.70        16.93         1.81        16.83 
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        56.58        13.45        41.49        45.60        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54         6.18 
TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       10.55        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
       14.40         6.71         7.99         2.37         4.11         5.88 
TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        0.23        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 
        9.60         7.56        12.23        19.20         3.45         4.41 
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-A6CV TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        13.61         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-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        41.10        28.14        35.38        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        18.71        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       34.78        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-A84R 
       28.08        24.16        40.83        24.79        33.24        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       14.93        23.80        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 
       25.87        33.93        61.41        26.99        31.36        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
       13.51         0.10        39.16        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-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        46.88        37.71        20.81 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.10              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            65.39            211.17 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           17.880            21.815 
[1] "0.1 - 65.4 (17.9)"  "0.0 - 211.2 (21.8)"
[1] "hr=" "2.8"
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    31  31
  6Q LOSS WILD-TYPE 197 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     31   31
  6Q LOSS WILD-TYPE  197  253
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              31               197
  MALE                31               253
[1] 2 2
[1] FALSE
D52V4, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    13  40
  6Q LOSS WILD-TYPE 171 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     13   40
  6Q LOSS WILD-TYPE  171  253
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               13               171
  YES              40               253
[1] 2 2
[1] FALSE
D52V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6Q LOSS MUTATED            37               10                15
  6Q LOSS WILD-TYPE         157              119               174
D52V6, multiclass
                   clus
vv                  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASTROCYTOMA                    37               157
  OLIGOASTROCYTOMA               10               119
  OLIGODENDROGLIOMA              15               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"
                   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                           5    55
  6Q LOSS WILD-TYPE                        16   417
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                      5                16
  WHITE                                         55               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"
D52V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     2  53
  6Q LOSS WILD-TYPE  30 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   53
  6Q LOSS WILD-TYPE   30  393
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                30
  NOT HISPANIC OR LATINO              53               393
[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 386 120
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               506 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1               120 
$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       31.69        24.43        26.17        24.99        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       21.57        95.11        20.98        22.29        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       17.16        21.30        17.98       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       95.57       130.78        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       51.88        15.32         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         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        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        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 
       21.53        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        18.64         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 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        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         7.99         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       85.55        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        18.54        28.37        27.16       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        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       25.87        33.93        61.41        26.99        31.36        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF 
       43.20        13.51         0.10         7.89        39.16        20.02 
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 

  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 
           20.810            20.895 
[1] "1.3 - 62.2 (20.8)"  "0.0 - 211.2 (20.9)"
[1] "hr=" "1.6"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   1
  7P LOSS WILD-TYPE 226 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    1
  7P LOSS WILD-TYPE  226  283
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               2               226
  MALE                 1               283
[1] 2 2
[1] FALSE
D53V4, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   2
  7P LOSS WILD-TYPE 184 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE  184  291
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0               184
  YES               2               291
[1] 2 2
[1] FALSE
D53V5, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               304 
       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-6401        TCGA-DU-6403 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6404        TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6410        TCGA-DU-7009        TCGA-DU-7011        TCGA-DU-7013 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299        TCGA-DU-7300 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304        TCGA-DU-7306 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161        TCGA-DU-8162 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8163        TCGA-DU-8165        TCGA-DU-8167        TCGA-DU-8168 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A6S2        TCGA-DU-A6S6        TCGA-DU-A6S7 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A6S8        TCGA-DU-A76R        TCGA-DU-A7T6        TCGA-DU-A7T8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7TA        TCGA-DU-A7TB        TCGA-DU-A7TC        TCGA-DU-A7TD 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7TG        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-E1-A7YE        TCGA-E1-A7YH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YI        TCGA-E1-A7YJ        TCGA-E1-A7YK        TCGA-E1-A7YL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YM        TCGA-E1-A7YN        TCGA-E1-A7YO        TCGA-E1-A7YQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7YS        TCGA-E1-A7YV        TCGA-E1-A7YW        TCGA-E1-A7YY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-A7Z2        TCGA-E1-A7Z4        TCGA-E1-A7Z6        TCGA-FG-5963 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-8181 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-A4MT        TCGA-FG-A4MW        TCGA-FG-A4MX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A60J        TCGA-FG-A60L        TCGA-FG-A6J1        TCGA-FG-A6J3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A711        TCGA-FG-A713        TCGA-FG-A87Q        TCGA-HT-7468 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7470        TCGA-HT-7475        TCGA-HT-7477        TCGA-HT-7481 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7482        TCGA-HT-7485        TCGA-HT-7607        TCGA-HT-7609 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7611        TCGA-HT-7686        TCGA-HT-7689        TCGA-HT-7692 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7854        TCGA-HT-7855 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7856        TCGA-HT-7858        TCGA-HT-7875        TCGA-HT-7884 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-8013        TCGA-HT-8105        TCGA-HT-8113        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-A7RG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RK        TCGA-TQ-A7RM        TCGA-TQ-A7RN        TCGA-TQ-A7RO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RP        TCGA-TQ-A7RQ        TCGA-TQ-A7RR        TCGA-TQ-A7RS 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TQ-A7RU        TCGA-TQ-A7RV        TCGA-TQ-A7RW        TCGA-TQ-A8XE 
"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-A8CF        TCGA-VM-A8CH        TCGA-WY-A858        TCGA-WY-A859 
"7P LOSS WILD-TYPE" "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         192              129               188
D53V6, multiclass
                   clus
vv                  7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASTROCYTOMA                     2               192
  OLIGOASTROCYTOMA                0               129
  OLIGODENDROGLIOMA               1               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                        21   469
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                21
  WHITE                                          3               469
[1] 4 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  32 444
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE   32  444
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               2               444
[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 386 120
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               506 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1               120 
$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        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 
        2.40        11.47        62.96       156.23       154.36        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        33.27        29.85        31.69 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       24.43        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       95.11        20.98        22.29        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
        7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
      130.78        14.30        29.13        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ 
       12.43        16.18        21.30        23.90        75.02        51.88 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       15.32         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         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        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        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        21.53 
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        18.64         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-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-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-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       85.55        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        18.54        28.37        27.16       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        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       25.87        33.93        61.41        26.99        31.36        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF 
       43.20        13.51         0.10         7.89        39.16        20.02 
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 

  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             20.81 
[1] "1.3 - 62.2 (42.0)"  "0.0 - 211.2 (20.8)"
[1] "hr=" "1.2"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   2
  7Q LOSS WILD-TYPE 227 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    2
  7Q LOSS WILD-TYPE  227  282
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               1               227
  MALE                 2               282
[1] 2 2
[1] FALSE
D54V4, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   2
  7Q LOSS WILD-TYPE 184 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    2
  7Q LOSS WILD-TYPE  184  291
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0               184
  YES               2               291
[1] 2 2
[1] FALSE
D54V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7Q LOSS MUTATED             2                0                 1
  7Q LOSS WILD-TYPE         192              129               188
D54V6, multiclass
                   clus
vv                  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASTROCYTOMA                     2               192
  OLIGOASTROCYTOMA                0               129
  OLIGODENDROGLIOMA               1               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                        21   469
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                21
  WHITE                                          3               469
[1] 4 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  32 443
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE   32  443
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               3               443
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    10   6
  8P LOSS WILD-TYPE 378 115
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16               493 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                6               115 
$`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-A7YQ TCGA-E1-A7YV TCGA-HT-7688 TCGA-HT-8564 TCGA-HT-A4DS 
       41.13        51.88        32.45        31.69        15.72         0.23 
TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-S9-A6WM TCGA-TQ-A7RR 
        1.28        14.53        19.86        25.87 

$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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 
       63.88        46.06         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        23.21        17.46        13.71        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         2.40        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76        17.16        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 
       51.52        37.38         7.50        44.42        38.89        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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
      130.78        14.30        29.13        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS 
       12.43        16.18        21.30        23.90        75.02        15.32 
TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
        0.76        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         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 
       52.21        36.82        18.77        14.93        42.54        41.33 
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 
       28.34        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        21.53        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 
       18.64         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-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-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 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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        41.10        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
      135.22        85.55        38.56        84.99        31.10        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        18.54        28.37        27.16       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        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        43.04        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        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 LOSS MUTATED 8P LOSS WILD-TYPE 
             0.23              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            51.88            211.17 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            19.91             20.98 
[1] "0.2 - 51.9 (19.9)"  "0.0 - 211.2 (21.0)"
[1] "hr=" "2.3"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     7  10
  8P LOSS WILD-TYPE 221 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7   10
  8P LOSS WILD-TYPE  221  274
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               7               221
  MALE                10               274
[1] 2 2
[1] FALSE
D55V4, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     2  12
  8P LOSS WILD-TYPE 182 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2   12
  8P LOSS WILD-TYPE  182  281
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                2               182
  YES              12               281
[1] 2 2
[1] FALSE
D55V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8P LOSS MUTATED             9                4                 4
  8P LOSS WILD-TYPE         185              125               185
D55V6, multiclass
                   clus
vv                  8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASTROCYTOMA                     9               185
  OLIGOASTROCYTOMA                4               125
  OLIGODENDROGLIOMA               4               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           2    14
  8P LOSS WILD-TYPE                        19   458
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                      2                19
  WHITE                                         14               458
[1] 4 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     2  15
  8P LOSS WILD-TYPE  30 431
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2   15
  8P LOSS WILD-TYPE   30  431
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                30
  NOT HISPANIC OR LATINO              15               431
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     7   4
  8Q LOSS WILD-TYPE 381 117
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               498 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               117 
$`8Q LOSS MUTATED`
TCGA-DH-5140 TCGA-DU-7006 TCGA-DU-8165 TCGA-E1-5304 TCGA-E1-A7YQ TCGA-HT-8564 
       19.96        11.47        19.13        41.13        51.88        15.72 
TCGA-HT-A4DS TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-S9-A6WM TCGA-TQ-A7RR 
        0.23         1.28        14.53        19.86        25.87 

$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        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 
        2.40        62.96       156.23       154.36        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        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
       22.29        11.41        26.76        17.16        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       38.89         0.56        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE 
      134.27        78.21        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
       93.21         3.65        19.46        12.43        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       23.90        75.02        15.32         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
      146.14        13.08        73.48       145.05        32.35        39.48 
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        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        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        28.34        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        21.53        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        18.64         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        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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-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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       85.55        38.56        84.99        31.10        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       18.64        14.07        36.13         7.92        26.93        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       19.99        20.02         8.19         2.04        20.68        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       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        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU 
       36.69        33.73        31.20        30.05        26.14        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        43.04        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        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 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.23              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            51.88            211.17 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           19.130            21.155 
[1] "0.2 - 51.9 (19.1)"  "0.0 - 211.2 (21.2)"
[1] "hr=" "2.7"
D56V2, continuous
D56V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6   5
  8Q LOSS WILD-TYPE 222 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6    5
  8Q LOSS WILD-TYPE  222  279
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               6               222
  MALE                 5               279
[1] 2 2
[1] FALSE
D56V4, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1   8
  8Q LOSS WILD-TYPE 183 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    8
  8Q LOSS WILD-TYPE  183  285
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                1               183
  YES               8               285
[1] 2 2
[1] FALSE
D56V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8Q LOSS MUTATED             5                3                 3
  8Q LOSS WILD-TYPE         189              126               186
D56V6, multiclass
                   clus
vv                  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASTROCYTOMA                     5               189
  OLIGOASTROCYTOMA                3               126
  OLIGODENDROGLIOMA               3               186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           1     9
  8Q LOSS WILD-TYPE                        20   463
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                      1                20
  WHITE                                          9               463
[1] 4 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     2   9
  8Q LOSS WILD-TYPE  30 437
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    9
  8Q LOSS WILD-TYPE   30  437
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                30
  NOT HISPANIC OR LATINO               9               437
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    72  44
  9P LOSS WILD-TYPE 316  77
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              116               393 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               44                77 
$`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        46.95 
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         2.40        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        33.96        20.98 
TCGA-DU-A6S8 TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 
       22.29        17.98        84.33         7.50         0.56        41.13 
TCGA-E1-5307 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YM 
       57.93        14.30        29.13         3.65        19.46        21.30 
TCGA-E1-A7YN TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7Z2 TCGA-EZ-7264 TCGA-F6-A8O4 
       23.90        51.88        15.32        13.08        39.48         0.20 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 
       25.48        36.82        42.54        18.44        17.88        14.24 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A711 TCGA-FG-A87Q TCGA-HT-7471 TCGA-HT-7477 
       18.38        18.71        48.69         5.72         0.13        24.26 
TCGA-HT-7606 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7902 TCGA-HT-8104 
       17.29         0.10        14.96         2.96        31.43        12.23 
TCGA-HT-8108 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HW-7490 TCGA-HW-8320 
        2.50        27.35         0.10         2.70        45.60        40.01 
TCGA-HW-8322 TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5F2 TCGA-P5-A5F4 
        6.18        20.71        19.00         0.23         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72Z TCGA-P5-A780 TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-RY-A83Z 
        1.28        11.64         2.37        14.53         9.17         9.90 
TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 
       62.17        41.10         7.92        26.93        19.99        20.02 
TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84J 
      169.84        99.06        31.59        65.39        30.44        24.16 
TCGA-TQ-A7RH TCGA-TQ-A7RP TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8CB TCGA-VM-A8CD 
       15.98        30.05        26.99        31.36         0.10         7.89 
TCGA-VM-A8CF TCGA-W9-A837 
       20.02        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        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.12       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 
       91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       13.71        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       154.36 
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 
       33.27        29.85        31.69        24.43        26.17        24.99 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       25.55        21.57        95.11        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI 
       21.30       139.04        51.52        37.38        44.42        38.89 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       50.14        67.46        79.99       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YH TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YO TCGA-E1-A7YU 
      130.78        93.21        12.43        16.18        75.02         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       32.45        36.82       146.14        73.48       145.05        32.35 
TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 
        0.23        47.77        52.21        18.77        14.93        41.33 
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        28.34        13.68 
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-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       10.72        23.70        14.76        17.82        21.53        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
       16.44        22.26        28.54        10.78        36.66        20.45 
TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       18.64        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-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-7607 
        5.03        29.85        23.18       122.47         4.57         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-7688 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       31.69         0.10         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-8010 TCGA-HT-8011 TCGA-HT-8012 
       35.47         3.72        11.28         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
       63.55         0.10        37.87        33.01         6.25         0.10 
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-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        0.07         5.33        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-7491 
       11.05         0.10        56.58        13.45        41.49        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK 
       69.27        35.44        39.75        42.54        10.55        12.76 
TCGA-HW-A5KL TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX 
       20.81        42.77        14.40        14.40         6.71         7.99 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72U TCGA-P5-A72W 
        2.37         2.30         4.11         5.88         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       13.25        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       12.23        19.20         3.45         4.41        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW 
       12.62        15.85        14.04        19.33        14.83        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-A840 
       94.03        32.65        59.38        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX 
        2.07        19.59        30.67        87.12        18.77        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IY 
       26.47        18.61        18.64        14.07        36.13        23.51 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z 
       27.16        10.39        30.05        98.63        18.71        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C 
       54.77        48.33        49.32        34.78        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       59.05        40.64        28.08        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-VM-A8C8 TCGA-VM-A8C9 
       26.14        25.87        33.93        61.41        43.04        43.20 
TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       13.51        39.16        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        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 

  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 
           20.365            21.300 
[1] "0.1 - 169.8 (20.4)" "0.0 - 211.2 (21.3)"
[1] "hr=" "2.4"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    52  65
  9P LOSS WILD-TYPE 176 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     52   65
  9P LOSS WILD-TYPE  176  219
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              52               176
  MALE                65               219
[1] 2 2
[1] FALSE
D57V4, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    26  79
  9P LOSS WILD-TYPE 158 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     26   79
  9P LOSS WILD-TYPE  158  214
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               26               158
  YES              79               214
[1] 2 2
[1] FALSE
D57V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9P LOSS MUTATED            55               23                39
  9P LOSS WILD-TYPE         139              106               150
D57V6, multiclass
                   clus
vv                  9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASTROCYTOMA                    55               139
  OLIGOASTROCYTOMA               23               106
  OLIGODENDROGLIOMA              39               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"
                   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                           7   105
  9P LOSS WILD-TYPE                        14   367
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                      7                14
  WHITE                                        105               367
[1] 4 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     6 102
  9P LOSS WILD-TYPE  26 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6  102
  9P LOSS WILD-TYPE   26  344
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                26
  NOT HISPANIC OR LATINO             102               344
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    30  20
  9Q LOSS WILD-TYPE 358 101
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50               459 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               20               101 
$`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        46.95        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        33.96        20.98        22.29        17.98 
TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-A7YD 
       84.33         7.50         0.56        41.13        57.93        14.30 
TCGA-E1-A7YE TCGA-E1-A7YN TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-EZ-7264 TCGA-F6-A8O4 
       29.13        23.90        51.88        15.32        39.48         0.20 
TCGA-FG-A87Q TCGA-HT-7471 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-A5RB 
        5.72         0.13         0.10        14.96         2.96         0.10 
TCGA-HT-A614 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-P5-A72Z TCGA-P5-A733 TCGA-QH-A6CV 
        2.70        19.00         1.28        11.64        13.61        14.53 
TCGA-QH-A6CZ TCGA-S9-A6U9 TCGA-S9-A7IS TCGA-S9-A7R1 TCGA-TM-A84H TCGA-TM-A84J 
        9.17        95.93         7.92       169.84        30.44        24.16 
TCGA-TM-A84T TCGA-TQ-A7RP 
       23.80        30.05 

$`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        49.94        49.12         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        91.13        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 
       63.88        46.06         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        23.21        17.46        13.71 
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         2.40        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        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        33.27        29.85        31.69        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K 
       26.17        24.99        25.55        21.57        95.11        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC 
       26.76        17.16        21.30       139.04        51.52        37.38 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 
       44.42        38.89        50.14        67.46        79.99       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
       78.21        95.57       130.78        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YV 
       12.43        16.18        21.30        75.02         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        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        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        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 
       21.53        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        18.64        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        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42        13.25        10.95 
TCGA-P5-A731 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
        9.01         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        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-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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61        35.15        98.24         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX 
       26.47        18.61        18.64        14.07        36.13        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        18.54        28.37        27.16        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        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       59.05        40.64        28.08        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       25.38        18.61        14.93        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       26.14        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        43.20        13.51         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        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 

  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 
           21.635            20.810 
[1] "0.1 - 169.8 (21.6)" "0.0 - 211.2 (20.8)"
[1] "hr=" "1.9"
D58V2, continuous
D58V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    22  28
  9Q LOSS WILD-TYPE 206 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     22   28
  9Q LOSS WILD-TYPE  206  256
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              22               206
  MALE                28               256
[1] 2 2
[1] FALSE
D58V4, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     8  33
  9Q LOSS WILD-TYPE 176 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   33
  9Q LOSS WILD-TYPE  176  260
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                8               176
  YES              33               260
[1] 2 2
[1] FALSE
D58V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9Q LOSS MUTATED            20               11                19
  9Q LOSS WILD-TYPE         174              118               170
D58V6, multiclass
                   clus
vv                  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASTROCYTOMA                    20               174
  OLIGOASTROCYTOMA               11               118
  OLIGODENDROGLIOMA              19               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"
                   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                           4    42
  9Q LOSS WILD-TYPE                        17   430
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                      4                17
  WHITE                                         42               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"
D58V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     3  45
  9Q LOSS WILD-TYPE  29 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3   45
  9Q LOSS WILD-TYPE   29  401
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                29
  NOT HISPANIC OR LATINO              45               401
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    35  48
  10P LOSS WILD-TYPE 353  73
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                83                426 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                48                 73 
$`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        33.96        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5311 TCGA-E1-A7YD TCGA-E1-A7YJ 
       21.30         7.50         0.56       134.27        14.30        19.46 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YQ TCGA-E1-A7Z2 TCGA-FG-6688 
       16.18        21.30        23.90        51.88        13.08        18.77 
TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q 
       18.44        20.09        10.72        18.38        10.78         5.72 
TCGA-HT-7471 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 
        0.13         0.23         0.49         3.72        16.24        12.23 
TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 
       13.78        15.72         0.23        27.35         5.33        16.14 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A72U TCGA-QH-A6CS 
       17.65         2.43        12.76        14.40         0.23        19.33 
TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM 
       14.53         5.03        62.17        24.39         5.85        19.86 
TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84I 
       26.93        10.39        18.71        54.77        24.92        28.08 
TCGA-TM-A84J TCGA-TQ-A7RM TCGA-TQ-A7RP TCGA-VM-A8CD TCGA-VW-A8FI 
       24.16        36.69        30.05         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        46.95         7.56 
TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 
       49.94        49.12         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        91.13        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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       46.06         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        23.21        17.46        13.71        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         2.40        62.96       156.23       154.36 
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        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       24.99        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       17.16        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42        38.89        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH 
       57.93        78.21        95.57       130.78        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
        3.65        12.43        75.02        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
       36.82       146.14        73.48       145.05        32.35        39.48 
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        52.21        36.82 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       14.93        42.54        41.33        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        28.34        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        21.53        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 
       28.54        36.66        48.69        20.45        18.64        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-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-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-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 
        5.33        35.47        11.28        31.43         1.64         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
       63.55         0.10        37.87        33.01         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         5.56         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB 
       28.27        26.04         0.13        20.22         0.07         0.10 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
        2.70        16.93         1.81        16.83        21.40        17.52 
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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM 
       40.01        42.54         6.18        10.55        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         7.99 
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        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.04        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-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        87.12        18.77        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       36.82        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
       95.93       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
       36.13         7.92        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
      169.84        99.06        30.05        98.63        31.59        20.48 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ 
        2.04        40.41        44.09        33.73        31.20        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       25.87        33.93        61.41        26.99        31.36        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       43.20        13.51         0.10        39.16        20.02        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 
             16.18              23.49 
[1] "0.1 - 134.3 (16.2)" "0.0 - 211.2 (23.5)"
[1] "hr=" "8.5"
D59V2, continuous
D59V3, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    38  45
  10P LOSS WILD-TYPE 190 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     38   45
  10P LOSS WILD-TYPE  190  239
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               38                190
  MALE                 45                239
[1] 2 2
[1] FALSE
D59V4, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    14  60
  10P LOSS WILD-TYPE 170 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     14   60
  10P LOSS WILD-TYPE  170  233
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                14                170
  YES               60                233
[1] 2 2
[1] FALSE
D59V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10P LOSS MUTATED            49               16                18
  10P LOSS WILD-TYPE         145              113               171
D59V6, multiclass
                   clus
vv                  10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASTROCYTOMA                     49                145
  OLIGOASTROCYTOMA                16                113
  OLIGODENDROGLIOMA               18                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"
                    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                           8    72
  10P LOSS WILD-TYPE                        13   400
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                       8                 13
  WHITE                                          72                400
[1] 4 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     4  74
  10P LOSS WILD-TYPE  28 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4   74
  10P LOSS WILD-TYPE   28  372
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 28
  NOT HISPANIC OR LATINO               74                372
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    42  54
  10Q LOSS WILD-TYPE 346  67
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                96                413 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                54                 67 
$`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        13.71 
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        33.96        11.41 
TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5311 TCGA-E1-A7YD 
       26.76        21.30         7.50         0.56       134.27        14.30 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YQ TCGA-E1-A7YV 
       19.46        16.18        21.30        23.90        51.88        32.45 
TCGA-E1-A7Z2 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-A4MU TCGA-FG-A4MW 
       13.08        18.77        18.44        20.09        10.72        18.38 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7471 TCGA-HT-7483 TCGA-HT-7857 
       22.26        10.78         5.72         0.13       172.77         0.23 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8564 
        0.49         3.72        16.24        12.23        13.78        15.72 
TCGA-HT-A4DS TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C 
        0.23        20.22        27.35         5.33        16.14        17.65 
TCGA-HT-A74H TCGA-HW-8321 TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EZ TCGA-P5-A72U 
        2.43        42.54        12.76        14.40         2.30         0.23 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6U0 
       19.33        14.53        12.23         5.03        62.17        24.39 
TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B 
        5.85        19.86        26.93        10.39        54.77        24.92 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TQ-A7RM TCGA-TQ-A7RP TCGA-VM-A8CD TCGA-VW-A8FI 
       28.08        24.16        36.69        30.05         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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06 
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 
       23.21        17.46        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         2.40        62.96 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 
      154.36       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 
       33.27        29.85        31.69        24.43        26.17        24.99 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O 
       25.55        21.57        95.11        20.98        22.29        17.16 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG 
       17.98       139.04        84.33        51.52        37.38        44.42 
TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       38.89        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       78.21        95.57       130.78        29.13        93.21         3.65 
TCGA-E1-A7YK TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY 
       12.43        75.02        15.32         0.76        36.82       146.14 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
       47.77        25.48        52.21        36.82        14.93        42.54 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 
       41.33        15.35        17.88        22.55        20.61        28.34 
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-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       32.61        38.27        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 
       21.53        15.02        16.44        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        18.64        27.52         0.10         6.67        11.54 
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-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
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-A5R9 
       29.59        34.19        28.27        26.04         0.13         0.07 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 
        0.10         2.70        16.93         1.81        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
       17.52        10.52        15.35        11.05         0.10        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM 
       39.75        40.01         6.18        10.55        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         7.99 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.37         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.83        13.61         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-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-A6U1 
       18.77        41.10        28.14        35.38        36.82        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       29.85        32.61        35.15        98.24        95.93       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 
       15.06        18.54        28.37        27.16       169.84        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        20.48        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       14.93        23.80        21.37        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       40.41        44.09        33.73        31.20        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        43.04        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10        39.16        20.02        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 
            16.535             23.470 
[1] "0.1 - 172.8 (16.5)" "0.0 - 211.2 (23.5)"
[1] "hr=" "5.1"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    45  51
  10Q LOSS WILD-TYPE 183 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     45   51
  10Q LOSS WILD-TYPE  183  233
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               45                183
  MALE                 51                233
[1] 2 2
[1] FALSE
D60V4, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    15  71
  10Q LOSS WILD-TYPE 169 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     15   71
  10Q LOSS WILD-TYPE  169  222
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                15                169
  YES               71                222
[1] 2 2
[1] FALSE
D60V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10Q LOSS MUTATED            56               19                21
  10Q LOSS WILD-TYPE         138              110               168
D60V6, multiclass
                   clus
vv                  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASTROCYTOMA                     56                138
  OLIGOASTROCYTOMA                19                110
  OLIGODENDROGLIOMA               21                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"
                    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                           8    85
  10Q LOSS WILD-TYPE                        13   387
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                       8                 13
  WHITE                                          85                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"
D60V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4  87
  10Q LOSS WILD-TYPE  28 359
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4   87
  10Q LOSS WILD-TYPE   28  359
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 28
  NOT HISPANIC OR LATINO               87                359
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    39  24
  11P LOSS WILD-TYPE 349  97
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                446 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                 97 
$`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        63.88        17.19        17.46 
TCGA-DH-A7UU TCGA-DU-6396 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
       13.71        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        29.85 
TCGA-DU-A5TS TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YK 
       31.69        50.14        41.13        29.13         3.65        12.43 
TCGA-E1-A7YL TCGA-E1-A7YV TCGA-FG-6689 TCGA-FG-A4MW TCGA-FG-A60L TCGA-HT-7470 
       16.18        32.45        14.93        18.38        21.53        40.11 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7601 TCGA-HT-7686 TCGA-HT-7693 TCGA-HT-7873 
       24.26         6.38         5.03        42.74        17.52        23.61 
TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A5R7 
       31.43        63.55        37.87         0.23        15.72        20.22 
TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HW-8319 TCGA-IK-7675 
        2.70         1.81        16.83        17.52        39.75        19.00 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-RY-A83Z TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A7R7 
        1.28         2.53         9.90        18.77        19.86        98.63 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A84I TCGA-TM-A84J 
       18.71        20.48        54.77        48.33        28.08        24.16 
TCGA-TQ-A7RR TCGA-VM-A8CF TCGA-WY-A859 
       25.87        20.02        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        46.95         7.56        49.94        49.12 
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 
       91.13        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        46.06 
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 
       23.21        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         2.40       154.36 
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        33.27 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       24.43        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       95.11        20.98        22.29        11.41        26.76        17.16 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 
        7.50        44.42        38.89         0.56        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD 
       57.93       134.27        78.21        95.57       130.78        14.30 
TCGA-E1-A7YH TCGA-E1-A7YJ TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ 
       93.21        19.46        21.30        23.90        75.02        51.88 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       15.32         0.76        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         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        52.21        36.82        18.77        42.54        41.33 
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 
       28.34        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-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       14.76        17.82        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        18.64         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 
       27.52         0.10         6.67        11.54         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 TCGA-HT-7480 
       16.54         3.75        17.42         6.54        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-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-7688 TCGA-HT-7689 
        0.76        44.68         6.05         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10         2.96         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 
       19.23        39.09         0.23        50.63         0.49        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-8015 TCGA-HT-8019 
       11.28         1.64        16.24         9.40         0.10        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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 
        0.13         0.07        27.35         0.10         5.33        16.93 
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        56.58        13.45        41.49        45.60 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       68.32        69.27        35.44        40.01        42.54         6.18 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X 
       10.55        12.76        20.81        20.71        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         7.99         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
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-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-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
       30.87         5.46        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        41.10        28.14        35.38        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       24.39        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       38.56        84.99        31.10        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       31.59        49.32        34.78        65.39        24.92        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       31.20        30.05        26.14        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       39.16        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       51.06        13.32        43.96        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       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 
            20.220             20.995 
[1] "0.2 - 156.2 (20.2)" "0.0 - 211.2 (21.0)"
[1] "hr=" "1.7"
D61V2, continuous
D61V3, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    32  31
  11P LOSS WILD-TYPE 196 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     32   31
  11P LOSS WILD-TYPE  196  253
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               32                196
  MALE                 31                253
[1] 2 2
[1] FALSE
D61V4, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    13  46
  11P LOSS WILD-TYPE 171 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13   46
  11P LOSS WILD-TYPE  171  247
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                13                171
  YES               46                247
[1] 2 2
[1] FALSE
D61V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11P LOSS MUTATED            37               14                12
  11P LOSS WILD-TYPE         157              115               177
D61V6, multiclass
                   clus
vv                  11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASTROCYTOMA                     37                157
  OLIGOASTROCYTOMA                14                115
  OLIGODENDROGLIOMA               12                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"
                    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    62
  11P LOSS WILD-TYPE                        20   410
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                 20
  WHITE                                          62                410
[1] 4 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     3  58
  11P LOSS WILD-TYPE  29 388
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3   58
  11P LOSS WILD-TYPE   29  388
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 29
  NOT HISPANIC OR LATINO               58                388
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    12   9
  11Q LOSS WILD-TYPE 376 112
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                488 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                112 
$`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-E1-A7YL TCGA-FG-A4MW TCGA-HT-7477 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8564 
       16.18        18.38        24.26        37.87         0.23        15.72 
TCGA-HT-A5R7 TCGA-HT-A614 TCGA-HT-A61B TCGA-P5-A5F6 TCGA-S9-A6TV TCGA-S9-A6WM 
       20.22         2.70        17.52         1.28        18.77        19.86 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84I 
       18.71        54.77        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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        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 
        2.40        62.96       156.23       154.36       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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76        17.16        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       95.57       130.78        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ 
       19.46        12.43        21.30        23.90        75.02        51.88 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       15.32         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         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        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        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-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        21.53        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        18.64         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-8019 TCGA-HT-8104 
       16.24         9.40        63.55         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-A616 
        0.07        27.35         0.10         5.33        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        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        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 
        7.99         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        0.76         0.23        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        3.45         2.37         4.41        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        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       31.59        20.48        48.33        49.32        34.78        65.39 
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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       25.87        33.93        61.41        26.99        31.36        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF 
       43.20        13.51         0.10         7.89        39.16        20.02 
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 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.23               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             54.77             211.17 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            18.710             21.385 
[1] "0.2 - 54.8 (18.7)"  "0.0 - 211.2 (21.4)"
[1] "hr=" "3.6"
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     9  12
  11Q LOSS WILD-TYPE 219 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      9   12
  11Q LOSS WILD-TYPE  219  272
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                9                219
  MALE                 12                272
[1] 2 2
[1] FALSE
D62V4, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3  15
  11Q LOSS WILD-TYPE 181 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   15
  11Q LOSS WILD-TYPE  181  278
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 3                181
  YES               15                278
[1] 2 2
[1] FALSE
D62V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11Q LOSS MUTATED            13                6                 2
  11Q LOSS WILD-TYPE         181              123               187
D62V6, multiclass
                   clus
vv                  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASTROCYTOMA                     13                181
  OLIGOASTROCYTOMA                 6                123
  OLIGODENDROGLIOMA                2                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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    21
  11Q LOSS WILD-TYPE                        21   451
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                 21
  WHITE                                          21                451
[1] 4 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  20
  11Q LOSS WILD-TYPE  31 426
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   20
  11Q LOSS WILD-TYPE   31  426
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 31
  NOT HISPANIC OR LATINO               20                426
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    19   6
  12P LOSS WILD-TYPE 369 115
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                25                484 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                115 
$`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         2.40        95.11 
TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-A7YH TCGA-E1-A7YS TCGA-E1-A7YV TCGA-FG-A6J3 
       21.30        50.14        93.21        15.32        32.45        22.26 
TCGA-HT-7470 TCGA-HT-7478 TCGA-HT-7686 TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-A5R7 
       40.11         6.38        42.74         0.10         2.50        20.22 
TCGA-HT-A61B TCGA-P5-A5EW TCGA-P5-A5F4 TCGA-P5-A72X TCGA-S9-A6U1 TCGA-S9-A7R4 
       17.52         6.71         0.76        13.25        25.81        30.05 
TCGA-S9-A89V 
       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        46.95         7.56        49.94        49.12 
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        91.13        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        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       46.06         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        23.21        17.46        13.71        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 
      154.36        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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       25.55        21.57        20.98        22.29        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       17.16        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42        38.89         0.56        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-A7YD TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       14.30        29.13         3.65        19.46        12.43        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YW 
       21.30        23.90        75.02        51.88         0.76        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
      146.14        13.08        73.48       145.05        32.35        39.48 
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        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        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        28.34        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        21.53        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        18.64         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-7477 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54        24.26        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-7687 TCGA-HT-7688 
       16.24         0.76        44.68         6.05         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-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
       12.23         6.25         0.46         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-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-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        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45        41.49        45.60        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         7.99         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 
        7.63         1.28         0.23        10.42        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        3.45         2.37         4.41        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        41.10        28.14        35.38        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       24.39        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R7 
       28.37        27.16       169.84        10.39        99.06        98.63 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        20.48        54.77        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.10               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             95.11             211.17 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            20.220             20.895 
[1] "0.1 - 95.1 (20.2)"  "0.0 - 211.2 (20.9)"
[1] "hr=" "1.3"
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    13  13
  12P LOSS WILD-TYPE 215 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     13   13
  12P LOSS WILD-TYPE  215  271
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               13                215
  MALE                 13                271
[1] 2 2
[1] FALSE
D63V4, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     7  18
  12P LOSS WILD-TYPE 177 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      7   18
  12P LOSS WILD-TYPE  177  275
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 7                177
  YES               18                275
[1] 2 2
[1] FALSE
D63V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12P LOSS MUTATED            15                5                 6
  12P LOSS WILD-TYPE         179              124               183
D63V6, multiclass
                   clus
vv                  12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASTROCYTOMA                     15                179
  OLIGOASTROCYTOMA                 5                124
  OLIGODENDROGLIOMA                6                183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           1    24
  12P LOSS WILD-TYPE                        20   448
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                       1                 20
  WHITE                                          24                448
[1] 4 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  25
  12P LOSS WILD-TYPE  32 421
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   25
  12P LOSS WILD-TYPE   32  421
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO               25                421
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    39  11
  12Q LOSS WILD-TYPE 349 110
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                50                459 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                11                110 
$`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         2.40        15.48        26.17        95.11 
TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-A7YH TCGA-E1-A7YK TCGA-E1-A7YS TCGA-E1-A7YV 
       21.30        50.14        93.21        12.43        15.32        32.45 
TCGA-E1-A7Z4 TCGA-FG-6689 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7686 
      145.05        14.93        40.11         3.75         6.38        42.74 
TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7902 TCGA-HT-8018 TCGA-HT-8106 TCGA-HT-8108 
       31.69         0.10        31.43        37.87         0.10         2.50 
TCGA-HT-A5R7 TCGA-HT-A618 TCGA-HT-A61B TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F4 
       20.22        16.83        17.52         6.71         2.30         0.76 
TCGA-P5-A72W TCGA-P5-A72X TCGA-S9-A6TV TCGA-S9-A6U1 TCGA-S9-A6WQ TCGA-S9-A7QX 
       10.42        13.25        18.77        25.81        14.07        18.54 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-TM-A84I TCGA-TQ-A7RR TCGA-VM-A8C8 
       30.05        98.63        18.71        28.08        25.87        43.04 
TCGA-WH-A86K TCGA-WY-A85B 
       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        46.95         7.56        49.94        49.12 
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        91.13 
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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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       154.36        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 
       33.27        29.85        31.69        24.43        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       25.55        21.57        20.98        22.29        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       17.16        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42        38.89         0.56        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-A7YD TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM 
       14.30        29.13         3.65        19.46        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY 
       23.90        75.02        51.88         0.76        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       13.08        73.48        32.35        39.48         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 
       47.77        25.48        52.21        36.82        18.77        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        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        21.53        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        18.64         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 
       11.54         0.13         0.03        16.54        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-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        6.05         0.10        14.96         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-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-8019 TCGA-HT-8104 
       16.24         9.40        63.55         0.10        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        6.25         0.46         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-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
        1.81        16.14        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        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX 
       19.00        42.77        14.40        14.40         0.23         7.99 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U 
        2.37         4.11         5.88         7.63         1.28         0.23 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        62.17        87.12        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       36.82        24.39        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.64        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY 
       20.02         8.19         2.04        20.68        15.06        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-S9-A89Z 
       27.16       169.84        10.39        99.06        31.59        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU 
       36.69        33.73        31.20        30.05        26.14        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       61.41        26.99        31.36        43.20        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        7.89        39.16        20.02        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21         8.05        51.06        43.96        39.88        43.40 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.10               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            145.05             211.17 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             20.76              20.81 
[1] "0.1 - 145.1 (20.8)" "0.0 - 211.2 (20.8)"
[1] "hr=" "1.1"
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    21  30
  12Q LOSS WILD-TYPE 207 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     21   30
  12Q LOSS WILD-TYPE  207  254
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               21                207
  MALE                 30                254
[1] 2 2
[1] FALSE
D64V4, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    14  35
  12Q LOSS WILD-TYPE 170 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     14   35
  12Q LOSS WILD-TYPE  170  258
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                14                170
  YES               35                258
[1] 2 2
[1] FALSE
D64V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12Q LOSS MUTATED            28               14                 9
  12Q LOSS WILD-TYPE         166              115               180
D64V6, multiclass
                   clus
vv                  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASTROCYTOMA                     28                166
  OLIGOASTROCYTOMA                14                115
  OLIGODENDROGLIOMA                9                180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           1    49
  12Q LOSS WILD-TYPE                        20   423
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                       1                 20
  WHITE                                          49                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"
D64V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  47
  12Q LOSS WILD-TYPE  31 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   47
  12Q LOSS WILD-TYPE   31  399
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 31
  NOT HISPANIC OR LATINO               47                399
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    80  36
  13Q LOSS WILD-TYPE 308  85
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               116                393 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                36                 85 
$`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        46.95         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        63.88        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5853 TCGA-DU-6392 
       27.81        17.19        13.71        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        31.69        21.57        20.98        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 
      139.04        84.33        50.14        67.46        41.13        57.93 
TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YL TCGA-E1-A7YQ 
      130.78        14.30        29.13        93.21        16.18        51.88 
TCGA-E1-A7YS TCGA-E1-A7YY TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 
       15.32       146.14        47.77        25.48        52.21        14.93 
TCGA-FG-6692 TCGA-FG-7641 TCGA-FG-8188 TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       18.44        20.61        14.96        14.76        21.53        15.02 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       22.26        10.78         5.72        11.54        40.11         0.13 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7604 TCGA-HT-7605 
        6.54        24.26       106.95       172.77       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7856 
       17.29        31.69        14.96         0.10         2.96        39.09 
TCGA-HT-7857 TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8564 TCGA-HT-A617 TCGA-HT-A61B 
        0.23        31.43         0.10        15.72        16.14        17.52 
TCGA-HW-7489 TCGA-HW-7491 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A72W 
       41.49        68.32        14.40         2.30         0.76        10.42 
TCGA-P5-A737 TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X8 
       12.23        14.04        14.53        13.61         2.20        16.73 
TCGA-RY-A83Z TCGA-RY-A847 TCGA-S9-A6UA TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
        9.90        30.67         5.85        26.93        23.51        20.02 
TCGA-S9-A7J3 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84F TCGA-TM-A84I 
       20.68        18.71        20.48        54.77        59.05        28.08 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RM TCGA-VM-A8CD 
       18.61        14.93        15.98        40.41        36.69         7.89 
TCGA-VM-A8CF TCGA-WY-A85E 
       20.02        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        49.94        49.12       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        91.13        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        46.06         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        23.21        17.46        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         2.40        62.96       154.36 
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        33.27        29.85        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       24.99        33.96        25.55        95.11        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       26.76        17.16        17.98        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
       44.42        38.89         0.56        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YN 
       95.57         3.65        19.46        12.43        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       75.02         0.76        32.45        36.82        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5965 
      145.05        32.35        39.48         0.23         0.20        36.82 
TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       18.77        42.54        41.33        15.35        17.88        22.55 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        28.34        13.68        14.24        16.01        20.09 
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-A6J1 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 
       23.70        17.82        16.44        28.54        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 
       20.45        18.64        27.52         0.10         6.67         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       16.54         3.75        17.42         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7607 
       95.93         4.01         5.03        29.85        23.18         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-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-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       19.23        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-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-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         6.25         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS 
       13.78         0.23        29.59        34.19        28.27         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-A618 TCGA-HT-A619 
        5.33         2.70        16.93         1.81        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-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       56.58        13.45        45.60        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        42.77        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 
        7.99         2.37         4.11         5.88         7.63         1.28 
TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        0.23        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        9.60         7.56        19.20         3.45         2.37         4.41 
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-A6CX TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 
       12.23         9.17        10.29        14.53        16.34         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-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       19.59        62.17        87.12        18.77        41.10        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       35.15        98.24        95.93       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       85.55        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IZ 
       18.61        18.64        14.07        36.13         7.92        19.99 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        8.19         2.04        15.06        18.54        28.37        27.16 
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-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        24.92        16.18 
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-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RK 
       25.38        23.80        21.37        19.69         2.04        44.09 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        43.04        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        0.10        39.16        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 
       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 
             19.99              22.06 
[1] "0.1 - 211.2 (20.0)" "0.0 - 182.3 (22.1)"
[1] "hr=" "1.2"
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    45  71
  13Q LOSS WILD-TYPE 183 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     45   71
  13Q LOSS WILD-TYPE  183  213
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               45                183
  MALE                 71                213
[1] 2 2
[1] FALSE
D65V4, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    28  84
  13Q LOSS WILD-TYPE 156 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     28   84
  13Q LOSS WILD-TYPE  156  209
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                28                156
  YES               84                209
[1] 2 2
[1] FALSE
D65V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  13Q LOSS MUTATED            49               27                40
  13Q LOSS WILD-TYPE         145              102               149
D65V6, multiclass
                   clus
vv                  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASTROCYTOMA                     49                145
  OLIGOASTROCYTOMA                27                102
  OLIGODENDROGLIOMA               40                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"
                    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                           6   107
  13Q LOSS WILD-TYPE                        15   365
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                       6                 15
  WHITE                                         107                365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     5 104
  13Q LOSS WILD-TYPE  27 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5  104
  13Q LOSS WILD-TYPE   27  342
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 27
  NOT HISPANIC OR LATINO              104                342
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    46  33
  14Q LOSS WILD-TYPE 342  88
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                79                430 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                33                 88 
$`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        49.94        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        63.88        46.06        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         2.40        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-E1-A7YD 
       22.29        26.76        21.30        79.99       130.78        14.30 
TCGA-E1-A7YH TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7Z2 TCGA-EZ-7264 
       93.21        21.30        51.88        15.32        13.08        39.48 
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        41.49        12.76        42.77         7.99 
TCGA-P5-A5EZ TCGA-P5-A77X TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CZ 
        2.30         3.45        19.33        14.53        13.61         9.17 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-S9-A6TS TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7QZ 
        9.90        28.08        62.17        19.86        26.93        27.16 
TCGA-S9-A7R2 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84I TCGA-TQ-A7RN 
       10.39        31.59        18.71        54.77        28.08        33.73 
TCGA-TQ-A7RR TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VV-A829 TCGA-WY-A858 
       25.87         0.10         7.89        20.02        37.05        43.96 
TCGA-WY-A85B 
       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 
       46.95         7.56        49.12         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        91.13        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 
       23.21        17.46        13.71        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 
      154.36       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        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       31.69        24.43        26.17        24.99        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A7T6 
       21.57        95.11        20.98        11.41        17.16        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 
       38.89         0.56        50.14        67.46        41.13        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ 
      134.27        78.21        95.57        29.13         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YV 
       12.43        16.18        23.90        75.02         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-F6-A8O3 
       36.82       146.14        73.48       145.05        32.35         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        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        14.96        22.52        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        21.53        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 
       18.64         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-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         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-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-7690 TCGA-HT-7691 TCGA-HT-7692 
        6.05        42.74         0.10         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-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-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-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-A619 TCGA-HT-A61B TCGA-HT-A74H 
        2.70        16.93         1.81        21.40        17.52         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        56.58        13.45 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       42.54         6.18        10.55        20.81        20.71        19.00 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5F0 
       14.40        14.40         0.23         6.71         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         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
        7.56        12.23        19.20         2.37         4.41        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CX 
        2.53        12.62        15.85        14.04        14.83        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-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-A843 TCGA-RY-A845 
       32.65        59.38        30.87         5.46         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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       85.55        38.56        84.99        31.10        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.64        14.07        36.13         7.92        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z 
       28.37       169.84        99.06        30.05        98.63        20.48 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        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-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       31.20        30.05        26.14        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH 
       31.36        43.04        43.20        13.51        39.16        23.47 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A859 
       16.01        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 

  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 
             21.30              20.81 
[1] "0.1 - 130.8 (21.3)" "0.0 - 211.2 (20.8)"
[1] "hr=" "2.6"
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    35  45
  14Q LOSS WILD-TYPE 193 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     35   45
  14Q LOSS WILD-TYPE  193  239
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               35                193
  MALE                 45                239
[1] 2 2
[1] FALSE
D66V4, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    23  51
  14Q LOSS WILD-TYPE 161 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     23   51
  14Q LOSS WILD-TYPE  161  242
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                23                161
  YES               51                242
[1] 2 2
[1] FALSE
D66V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  14Q LOSS MUTATED            37               18                25
  14Q LOSS WILD-TYPE         157              111               164
D66V6, multiclass
                   clus
vv                  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASTROCYTOMA                     37                157
  OLIGOASTROCYTOMA                18                111
  OLIGODENDROGLIOMA               25                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           4    71
  14Q LOSS WILD-TYPE                        17   401
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                       4                 17
  WHITE                                          71                401
[1] 4 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     3  67
  14Q LOSS WILD-TYPE  29 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3   67
  14Q LOSS WILD-TYPE   29  379
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 29
  NOT HISPANIC OR LATINO               67                379
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    35  15
  15Q LOSS WILD-TYPE 353 106
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                50                459 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                15                106 
$`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        63.88 
TCGA-DH-A669 TCGA-DH-A7UT TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-7007 TCGA-DU-8158 
       30.21        17.46        52.11         1.22        62.96         5.10 
TCGA-DU-A6S3 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TC TCGA-E1-5311 TCGA-E1-A7YK 
       21.57        21.30        17.98        37.38       134.27        12.43 
TCGA-E1-A7YS TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-HT-7468 
       15.32        15.35        17.88        18.38        22.26         6.67 
TCGA-HT-7480 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-8012 TCGA-HT-A618 
       75.19        17.29        45.99         0.23         9.40        16.83 
TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A74K TCGA-P5-A5EZ TCGA-P5-A77W TCGA-QH-A65S 
       21.40        17.52        15.35         2.30        19.20         2.53 
TCGA-QH-A6X8 TCGA-RY-A83X TCGA-S9-A6TS TCGA-S9-A6U2 TCGA-S9-A6WD TCGA-S9-A6WI 
       16.73        30.87        62.17        29.85        75.25        84.99 
TCGA-S9-A7QZ TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TQ-A7RO TCGA-VM-A8CF TCGA-VV-A86M 
       27.16        20.48        49.32        31.20        20.02        16.01 
TCGA-W9-A837 TCGA-WY-A85D 
       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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
       49.12         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        91.13        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        46.06         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        23.21        13.71 
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         2.40        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      154.36        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        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       31.69        24.43        26.17        24.99        33.96        25.55 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       95.11        20.98        22.29        11.41        26.76        17.16 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
      139.04        84.33        51.52         7.50        44.42        38.89 
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-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
        3.65        19.46        16.18        21.30        23.90        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       51.88         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         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        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       42.54        41.33        18.44        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       28.34        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-A70Y 
       14.76        17.82        21.53        15.02        16.44        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        18.64         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
       27.52         0.10        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-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-7607 TCGA-HT-7608 
       29.85        23.18       122.47         4.57         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-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-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-A61C TCGA-HT-A74H 
        2.70        16.93         1.81        16.14        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       10.52        11.05         0.10        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        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 
        7.99         2.37         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         0.23        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77X 
        9.01        13.61         9.60         7.56        12.23         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        2.37         4.41        15.16        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-A6X9 TCGA-QH-A6XA 
        9.17        10.29        14.53        16.34         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-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       59.38         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        41.10        28.14        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       36.82        24.39        25.81        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
       95.93         5.85       123.65       135.22        85.55        38.56 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
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-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       18.71        54.77        48.33        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       44.09        36.69        33.73        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        43.04        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        39.16        23.47        37.05 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21         8.05        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85E 
       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 
             20.89              20.81 
[1] "0.2 - 134.3 (20.9)" "0.0 - 211.2 (20.8)"
[1] "hr=" "1.3"
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    21  30
  15Q LOSS WILD-TYPE 207 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     21   30
  15Q LOSS WILD-TYPE  207  254
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               21                207
  MALE                 30                254
[1] 2 2
[1] FALSE
D67V4, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    22  24
  15Q LOSS WILD-TYPE 162 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     22   24
  15Q LOSS WILD-TYPE  162  269
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                22                162
  YES               24                269
[1] 2 2
[1] FALSE
D67V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  15Q LOSS MUTATED            17               12                22
  15Q LOSS WILD-TYPE         177              117               167
D67V6, multiclass
                   clus
vv                  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASTROCYTOMA                     17                177
  OLIGOASTROCYTOMA                12                117
  OLIGODENDROGLIOMA               22                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"
                    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                           2    46
  15Q LOSS WILD-TYPE                        19   426
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                       2                 19
  WHITE                                          46                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"
D67V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2  46
  15Q LOSS WILD-TYPE  30 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   46
  15Q LOSS WILD-TYPE   30  400
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 30
  NOT HISPANIC OR LATINO               46                400
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     7   7
  16P LOSS WILD-TYPE 381 114
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                495 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 7                114 
$`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-E1-A7YQ TCGA-FG-A4MW TCGA-HT-7477 TCGA-HT-8564 TCGA-P5-A780 TCGA-S9-A7IX 
       51.88        18.38        24.26        15.72         2.37        26.93 
TCGA-S9-A89V TCGA-TQ-A7RM 
       18.71        36.69 

$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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 
       63.88        46.06         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        23.21        17.46        13.71        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         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       154.36        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        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76        17.16        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       95.57       130.78        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO 
       19.46        12.43        16.18        21.30        23.90        75.02 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       15.32         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         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        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        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-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        21.53        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        18.64         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-A4DS 
       13.78         0.23        29.59        34.19        28.27         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        56.58        13.45        41.49        45.60 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       68.32        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
        6.18        10.55        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         7.99 
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         0.23        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        3.45         4.41        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-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        26.47        18.61        18.64 
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        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        20.48        54.77        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
        2.04        40.41        44.09        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       26.14        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        43.20        13.51         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        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 
              2.37               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             78.28             211.17 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             28.57              20.71 
[1] "2.4 - 78.3 (28.6)"  "0.0 - 211.2 (20.7)"
[1] "hr=" "2.1"
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     6   8
  16P LOSS WILD-TYPE 222 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      6    8
  16P LOSS WILD-TYPE  222  276
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                6                222
  MALE                  8                276
[1] 2 2
[1] FALSE
D68V4, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  11
  16P LOSS WILD-TYPE 181 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   11
  16P LOSS WILD-TYPE  181  282
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 3                181
  YES               11                282
[1] 2 2
[1] FALSE
D68V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16P LOSS MUTATED             7                3                 4
  16P LOSS WILD-TYPE         187              126               185
D68V6, multiclass
                   clus
vv                  16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASTROCYTOMA                      7                187
  OLIGOASTROCYTOMA                 3                126
  OLIGODENDROGLIOMA                4                185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           1    13
  16P LOSS WILD-TYPE                        20   459
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                       1                 20
  WHITE                                          13                459
[1] 4 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     2  12
  16P LOSS WILD-TYPE  30 434
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2   12
  16P LOSS WILD-TYPE   30  434
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 30
  NOT HISPANIC OR LATINO               12                434
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    12  10
  16Q LOSS WILD-TYPE 376 111
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                487 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                111 
$`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-E1-A7YQ TCGA-FG-A4MW 
       30.67        19.13        15.48        57.93        51.88        18.38 
TCGA-HT-7469 TCGA-HT-8564 TCGA-HT-A4DS TCGA-P5-A780 TCGA-S9-A6U9 TCGA-S9-A6WH 
       11.54        15.72         0.23         2.37        95.93        38.56 
TCGA-S9-A7IX TCGA-S9-A89V TCGA-S9-A89Z TCGA-TQ-A7RM 
       26.93        18.71        20.48        36.69 

$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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 
       63.88        46.06         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        23.21        17.46        13.71        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         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 
      156.23       154.36        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        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
       22.29        11.41        26.76        17.16        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       38.89         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE 
      134.27        78.21        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
       93.21         3.65        19.46        12.43        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       23.90        75.02        15.32         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
      146.14        13.08        73.48       145.05        32.35        39.48 
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        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        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        28.34        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 
       21.53        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        18.64         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-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-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-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        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.60        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54         6.18        10.55        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 
        7.99         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         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
       19.20         3.45         4.41        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        41.10        28.14        35.38        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       24.39        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI 
        5.85       123.65        75.25       135.22        85.55        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
       36.13         7.92        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
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-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       44.09        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        43.04        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        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 
            23.705             20.810 
[1] "0.2 - 117.4 (23.7)" "0.0 - 211.2 (20.8)"
[1] "hr=" "1.8"
D69V2, continuous
D69V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    11  11
  16Q LOSS WILD-TYPE 217 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     11   11
  16Q LOSS WILD-TYPE  217  273
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               11                217
  MALE                 11                273
[1] 2 2
[1] FALSE
D69V4, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3  18
  16Q LOSS WILD-TYPE 181 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   18
  16Q LOSS WILD-TYPE  181  275
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 3                181
  YES               18                275
[1] 2 2
[1] FALSE
D69V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16Q LOSS MUTATED            11                5                 6
  16Q LOSS WILD-TYPE         183              124               183
D69V6, multiclass
                   clus
vv                  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASTROCYTOMA                     11                183
  OLIGOASTROCYTOMA                 5                124
  OLIGODENDROGLIOMA                6                183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           2    20
  16Q LOSS WILD-TYPE                        19   452
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                       2                 19
  WHITE                                          20                452
[1] 4 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     2  20
  16Q LOSS WILD-TYPE  30 426
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2   20
  16Q LOSS WILD-TYPE   30  426
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 30
  NOT HISPANIC OR LATINO               20                426
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    10   3
  17P LOSS WILD-TYPE 378 118
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                496 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                118 
$`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        33.27        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 
TCGA-TQ-A7RI 
        2.04 

$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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 
        2.40        11.47        62.96       156.23       154.36       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 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76        17.16        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN 
        3.65        19.46        12.43        16.18        21.30        23.90 
TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       75.02        51.88        15.32         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
      146.14        13.08        73.48       145.05        32.35        39.48 
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        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        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        28.34        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-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       21.53        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        18.64         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-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        31.69         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-8107 TCGA-HT-8108 
       37.87        33.01        12.23         6.25         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        56.58        13.45        41.49        45.60 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       68.32        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
        6.18        10.55        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         7.99 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U 
        2.37         4.11         5.88         7.63         0.76         0.23 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        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 
       41.10        28.14        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       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        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
       15.98        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             33.27             211.17 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             14.96              21.30 
[1] "0.1 - 33.3 (15.0)"  "0.0 - 211.2 (21.3)"
[1] "hr=" "3.2"
D70V2, continuous
D70V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     8   5
  17P LOSS WILD-TYPE 220 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      8    5
  17P LOSS WILD-TYPE  220  279
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                8                220
  MALE                  5                279
[1] 2 2
[1] FALSE
D70V4, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4   6
  17P LOSS WILD-TYPE 180 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    6
  17P LOSS WILD-TYPE  180  287
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                180
  YES                6                287
[1] 2 2
[1] FALSE
D70V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17P LOSS MUTATED             6                2                 5
  17P LOSS WILD-TYPE         188              127               184
D70V6, multiclass
                   clus
vv                  17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASTROCYTOMA                      6                188
  OLIGOASTROCYTOMA                 2                127
  OLIGODENDROGLIOMA                5                184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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    13
  17P LOSS WILD-TYPE                        21   459
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                 21
  WHITE                                          13                459
[1] 4 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     3  10
  17P LOSS WILD-TYPE  29 436
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3   10
  17P LOSS WILD-TYPE   29  436
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 29
  NOT HISPANIC OR LATINO               10                436
[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 381 120
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                501 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                120 
$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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 
        2.40        11.47        62.96       156.23       154.36        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        33.27        29.85        31.69        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       26.17        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
       20.98        22.29        11.41        26.76        17.16        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK 
       14.30        29.13        93.21         3.65        19.46        12.43 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS 
       16.18        21.30        23.90        75.02        51.88        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
        0.76        32.45        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         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        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        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-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        14.76        17.82        21.53        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 
       18.64         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-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-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 
       56.58        13.45        41.49        45.60        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54         6.18        10.55 
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         7.99         2.37         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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        41.10        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       26.93        23.51        19.99        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       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 
       20.48        54.77        48.33        49.32        34.78        65.39 
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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       14.93        23.80        21.37        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       40.41        44.09        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       26.14        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        43.20        13.51         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        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 

  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              21.30 
[1] "0.1 - 23.7 (8.6)"   "0.0 - 211.2 (21.3)"
[1] "hr=" "2.2"
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4   4
  17Q LOSS WILD-TYPE 224 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    4
  17Q LOSS WILD-TYPE  224  280
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                4                224
  MALE                  4                280
[1] 2 2
[1] FALSE
D71V4, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3   3
  17Q LOSS WILD-TYPE 181 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    3
  17Q LOSS WILD-TYPE  181  290
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 3                181
  YES                3                290
[1] 2 2
[1] FALSE
D71V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17Q LOSS MUTATED             3                1                 4
  17Q LOSS WILD-TYPE         191              128               185
D71V6, multiclass
                   clus
vv                  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASTROCYTOMA                      3                191
  OLIGOASTROCYTOMA                 1                128
  OLIGODENDROGLIOMA                4                185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                        21   464
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                 21
  WHITE                                           8                464
[1] 4 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  30 440
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    6
  17Q LOSS WILD-TYPE   30  440
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 30
  NOT HISPANIC OR LATINO                6                440
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    50  18
  18P LOSS WILD-TYPE 338 103
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                68                441 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                103 
$`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        63.88        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       154.36       117.40        62.01 
TCGA-DU-8158 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A7T6 TCGA-E1-5307 TCGA-E1-A7YL 
        5.10        29.85        24.43        17.98        57.93        16.18 
TCGA-E1-A7YM TCGA-E1-A7YS TCGA-FG-8188 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7480 
       21.30        15.32        14.96         6.54        24.26        75.19 
TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7857 TCGA-HT-7858 
       45.99         0.23        31.69         2.96         0.23        50.63 
TCGA-HT-8564 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A74L TCGA-HW-7491 
       15.72         0.10         1.81        16.14        11.05        68.32 
TCGA-HW-8320 TCGA-HW-A5KK TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A72Z TCGA-P5-A780 
       40.01        12.76         7.99         2.30        11.64         2.37 
TCGA-QH-A65R TCGA-QH-A65Z TCGA-RY-A840 TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6TX 
       15.16        14.04        28.08        62.17        41.10        28.14 
TCGA-S9-A6UA TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
        5.85        75.25        38.56        31.10        19.86        26.47 
TCGA-S9-A6WP TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A84G TCGA-TM-A84I 
       18.64        28.37        10.39        18.71        40.64        28.08 
TCGA-TQ-A7RF TCGA-VM-A8CA 
       21.37        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        46.95         7.56        49.94        49.12         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        91.13 
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        46.06 
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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
       17.46        13.71        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         2.40        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        33.27        31.69        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
       22.29        11.41        26.76        17.16        21.30       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ 
        3.65        19.46        12.43        23.90        75.02        51.88 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
        0.76        32.45        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         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        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        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        28.34        13.68        14.24        16.01        20.09 
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        21.53        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 
       18.64         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-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        6.38        40.34        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-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 
        3.16        22.06        56.09        57.60        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-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-7856 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.48        19.23        39.09         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-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       34.19        28.27         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A618 
        0.07        27.35         5.33         2.70        16.93        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-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 
        0.10        56.58        13.45        41.49        45.60        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL 
       35.44        39.75        42.54         6.18        10.55        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-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        6.71         2.37         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 
        1.28         0.23        10.42        13.25        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A781 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU 
        4.41         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-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-A843 TCGA-RY-A845 TCGA-RY-A847 
       30.87         5.46         9.90         2.07        19.59        30.67 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       87.12        18.77        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       29.85        32.61        35.15        98.24        95.93       123.65 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ 
      135.22        85.55        84.99        18.61        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        20.68        15.06        18.54        27.16       169.84 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       99.06        30.05        98.63        31.59        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       59.05        30.44        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RG TCGA-TQ-A7RH 
       25.38        18.61        14.93        23.80        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       31.36        43.04        43.20         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        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 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.10               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            154.36             211.17 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             24.23              20.68 
[1] "0.1 - 154.4 (24.2)" "0.0 - 211.2 (20.7)"
[1] "hr=" "1.1"
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    24  44
  18P LOSS WILD-TYPE 204 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     24   44
  18P LOSS WILD-TYPE  204  240
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               24                204
  MALE                 44                240
[1] 2 2
[1] FALSE
D72V4, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    24  38
  18P LOSS WILD-TYPE 160 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     24   38
  18P LOSS WILD-TYPE  160  255
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                24                160
  YES               38                255
[1] 2 2
[1] FALSE
D72V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18P LOSS MUTATED            27               11                30
  18P LOSS WILD-TYPE         167              118               159
D72V6, multiclass
                   clus
vv                  18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASTROCYTOMA                     27                167
  OLIGOASTROCYTOMA                11                118
  OLIGODENDROGLIOMA               30                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"
                    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                           1    63
  18P LOSS WILD-TYPE                        20   409
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                       1                 20
  WHITE                                          63                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"
D72V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  58
  18P LOSS WILD-TYPE  29 388
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   58
  18P LOSS WILD-TYPE   29  388
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 29
  NOT HISPANIC OR LATINO               58                388
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    46  16
  18Q LOSS WILD-TYPE 342 105
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                447 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                16                105 
$`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        63.88        30.21        42.05        17.46 
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       154.36       117.40 
TCGA-DU-7300 TCGA-DU-8158 TCGA-DU-A5TT TCGA-DU-A7T6 TCGA-E1-5307 TCGA-E1-A7YM 
       62.01         5.10        24.43        17.98        57.93        21.30 
TCGA-E1-A7YS TCGA-FG-8188 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7606 
       15.32        14.96         6.54        24.26        75.19        17.29 
TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7857 TCGA-HT-8564 
       45.99         0.23        31.69         2.96         0.23        15.72 
TCGA-HT-A5RB TCGA-HT-A617 TCGA-HT-A74L TCGA-HW-7491 TCGA-HW-8320 TCGA-P5-A5EX 
        0.10        16.14        11.05        68.32        40.01         7.99 
TCGA-P5-A72Z TCGA-QH-A65R TCGA-QH-A65Z TCGA-RY-A840 TCGA-S9-A6TS TCGA-S9-A6TW 
       11.64        15.16        14.04        28.08        62.17        41.10 
TCGA-S9-A6TX TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       28.14        75.25        38.56        31.10        19.86        26.47 
TCGA-S9-A6WP TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-TM-A84G TCGA-TM-A84I TCGA-TQ-A7RF 
       18.64        28.37        10.39        40.64        28.08        21.37 
TCGA-TQ-A7RI TCGA-VM-A8CA 
        2.04        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        46.95         7.56        49.94        49.12 
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 
       91.13        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 
       46.06         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 
       23.21        13.71        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         2.40        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        33.27        29.85        31.69        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
       22.29        11.41        26.76        17.16        21.30       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
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-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YN TCGA-E1-A7YO 
        3.65        19.46        12.43        16.18        23.90        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       51.88         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         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        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        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        21.53        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        18.64         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-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       17.42         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-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 
        3.16        22.06        56.09        57.60        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-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-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-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-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-A5RC TCGA-HT-A614 TCGA-HT-A615 
       20.22         0.07        27.35         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
        1.81        16.83        21.40        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       10.52        15.35         0.10        56.58        13.45        41.49 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-8322 
       45.60        69.27        35.44        39.75        42.54         6.18 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40        14.40         0.23         6.71         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         0.23 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       10.42        13.25        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        15.85        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-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU 
        5.46         9.90         2.07        19.59        30.67        87.12 
TCGA-S9-A6TV TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       18.77        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ 
      135.22        85.55        84.99        18.61        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        20.68        15.06        18.54        27.16       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        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       16.18        59.05        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-A7RG 
       33.24        25.38        18.61        14.93        23.80        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
       15.98        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       31.36        43.04        43.20         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        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 

  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 
             25.45              20.61 
[1] "0.1 - 182.3 (25.4)" "0.0 - 211.2 (20.6)"
[1] "hr=" "1.1"
D73V2, continuous
D73V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    25  37
  18Q LOSS WILD-TYPE 203 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     25   37
  18Q LOSS WILD-TYPE  203  247
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               25                203
  MALE                 37                247
[1] 2 2
[1] FALSE
D73V4, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    21  36
  18Q LOSS WILD-TYPE 163 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     21   36
  18Q LOSS WILD-TYPE  163  257
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                21                163
  YES               36                257
[1] 2 2
[1] FALSE
D73V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18Q LOSS MUTATED            20               10                32
  18Q LOSS WILD-TYPE         174              119               157
D73V6, multiclass
                   clus
vv                  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASTROCYTOMA                     20                174
  OLIGOASTROCYTOMA                10                119
  OLIGODENDROGLIOMA               32                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"
                    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                           1    57
  18Q LOSS WILD-TYPE                        20   415
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                       1                 20
  WHITE                                          57                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"
D73V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4  53
  18Q LOSS WILD-TYPE  28 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4   53
  18Q LOSS WILD-TYPE   28  393
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 28
  NOT HISPANIC OR LATINO               53                393
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    19   6
  19P LOSS WILD-TYPE 369 115
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                25                484 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                115 
$`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        63.88         8.02        42.05 
TCGA-DU-5855 TCGA-DU-A5TS TCGA-E1-5318 TCGA-E1-A7YK TCGA-HT-7688 TCGA-HT-7857 
        6.81        31.69        78.21        12.43        31.69         0.23 
TCGA-HT-8111 TCGA-HT-8564 TCGA-P5-A5F6 TCGA-R8-A6MO TCGA-RY-A840 TCGA-S9-A6TX 
        0.23        15.72         1.28        32.65        28.08        28.14 
TCGA-S9-A6WI TCGA-S9-A7IS TCGA-TM-A84M TCGA-TQ-A7RH TCGA-TQ-A7RM TCGA-TQ-A7RO 
       84.99         7.92        24.79        15.98        36.69        31.20 
TCGA-WY-A858 
       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        46.95         7.56        49.94        49.12 
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 
       91.13        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        46.06 
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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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 
        2.40        11.47        62.96       156.23       154.36        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        33.27        29.85        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       26.17        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
       20.98        22.29        11.41        26.76        17.16        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       44.42        38.89         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD 
       79.99        57.93       134.27        95.57       130.78        14.30 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM 
       29.13        93.21         3.65        19.46        16.18        21.30 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       23.90        75.02        51.88        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       39.48         0.23         0.20        47.77        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        42.54        41.33        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        28.34 
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        21.53        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        18.64 
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-7689 TCGA-HT-7690 
       44.68         6.05        42.74         0.10        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-7860 TCGA-HT-7873 TCGA-HT-7874 
       19.23        39.09        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-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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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         7.99         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-A72Z 
        7.63         0.76         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       19.20         3.45         2.37         4.41        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-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       12.99        88.83        94.03        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
        9.90         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        41.10        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WL 
      123.65        75.25       135.22        85.55        38.56        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       26.93        23.51        19.99        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       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 
       20.48        54.77        48.33        49.32        34.78        65.39 
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-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       24.16        40.83        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       23.80        21.37        19.69         2.04        40.41        44.09 
TCGA-TQ-A7RN TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       33.73        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       26.99        31.36        43.04        43.20        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        7.89        39.16        20.02        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 
            28.140             20.695 
[1] "0.2 - 85.0 (28.1)"  "0.0 - 211.2 (20.7)"
[1] "hr=" "1.1"
D74V2, continuous
D74V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    11  14
  19P LOSS WILD-TYPE 217 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     11   14
  19P LOSS WILD-TYPE  217  270
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               11                217
  MALE                 14                270
[1] 2 2
[1] FALSE
D74V4, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     7  16
  19P LOSS WILD-TYPE 177 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7   16
  19P LOSS WILD-TYPE  177  277
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 7                177
  YES               16                277
[1] 2 2
[1] FALSE
D74V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19P LOSS MUTATED             9                7                 9
  19P LOSS WILD-TYPE         185              122               180
D74V6, multiclass
                   clus
vv                  19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASTROCYTOMA                      9                185
  OLIGOASTROCYTOMA                 7                122
  OLIGODENDROGLIOMA                9                180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           4    19
  19P LOSS WILD-TYPE                        17   453
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                       4                 17
  WHITE                                          19                453
[1] 4 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     4  18
  19P LOSS WILD-TYPE  28 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   18
  19P LOSS WILD-TYPE   28  428
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 28
  NOT HISPANIC OR LATINO               18                428
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED   171  36
  19Q LOSS WILD-TYPE 217  85
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               207                302 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                36                 85 
$`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        49.94         6.61 
TCGA-DB-5274 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG 
       75.25        50.86        91.13        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 
       63.88         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        23.21        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       154.36       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        31.69        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TC 
       21.57        95.11        22.29        21.30        17.98        37.38 
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-A7YK TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YY TCGA-EZ-7264 
      130.78        12.43        75.02        15.32       146.14        39.48 
TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
        0.23        47.77        52.21        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-A4MT TCGA-FG-A60K 
       20.61        16.01        20.09        14.96        38.27        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-7469 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 
       11.54         0.13        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-7688 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 
       31.69         2.96         6.90        14.53        39.09         0.23 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 
       37.15         0.33         0.13        35.47         1.64         9.40 
TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R9 
        6.25         5.56         0.23        15.72        26.04         0.07 
TCGA-HT-A615 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 
       16.93        21.40        17.52        15.35        11.05        56.58 
TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 
       13.45        68.32        35.44         6.18        10.55        42.77 
TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-P5-A5F6 TCGA-P5-A72Z TCGA-P5-A730 
       14.40         7.99         4.11         1.28        11.64        10.95 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V 
       12.23        19.20         3.45         4.41        15.16        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 
       15.85        14.04        14.83         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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD 
       28.14        35.38        29.85        32.61       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP 
      135.22        38.56        84.99        31.10        26.47        18.64 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       36.13         7.92        23.51         8.19         2.04        20.68 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M 
       28.37        27.16       169.84        49.32        40.64        24.79 
TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       33.24        18.61        14.93        19.69        15.98         2.04 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RW 
       36.69        33.73        31.20        26.14        33.93        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 
       31.36        43.04        13.51         0.10        39.16        37.05 
TCGA-VW-A7QS TCGA-W9-A837 TCGA-WY-A858 
       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        46.95 
TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.56        49.12       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        46.06        17.46        13.71        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 
        2.40        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 
       33.27        29.85        24.43        26.17        24.99        33.96 
TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TA 
       20.98        11.41        26.76        17.16       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       51.52         7.50        38.89         0.56        50.14        67.46 
TCGA-E1-5307 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
       57.93        14.30        29.13        93.21         3.65        19.46 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV 
       16.18        21.30        23.90        51.88         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-F6-A8O4 
       36.82        13.08        73.48       145.05        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        42.54        41.33 
TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8189 
       18.44        20.09        28.34        13.68        14.24        22.52 
TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       32.61        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87N 
       21.53        22.26        28.54        10.78        48.69        18.64 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        5.72        27.52        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-7482 
       17.42         6.54        24.26         6.38        40.34       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-7606 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 
       17.29        45.99        56.09        57.60         0.16         0.76 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 
        6.05        42.74        14.96         0.10         0.10        17.52 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 
       39.48        19.23        50.63         0.49        23.61         3.68 
TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 
        5.33         3.72        11.28        31.43        16.24        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS 
        2.50        13.78        29.59        34.19        28.27         0.23 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13        20.22        27.35         0.10         5.33         2.70 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
        1.81        16.14        16.83        17.65         2.43        10.52 
TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 
        0.10        41.49        45.60        69.27        39.75        40.01 
TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 
       42.54        12.76        20.81        20.71        19.00        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 
        0.23         6.71         2.37         2.30         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A731 TCGA-P5-A733 
        0.76         0.23        10.42        13.25         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A780 TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CV 
        9.60         7.56         2.37         2.53        19.33        14.53 
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        36.82        24.39        25.81        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WQ 
       95.93         5.85        85.55        19.86        18.61        14.07 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R2 
       26.93        19.99        20.02        15.06        18.54        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        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       54.77        48.33        34.78        65.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84Q 
       59.05        30.44        28.08        24.16        40.83        25.38 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RP TCGA-TQ-A7RR 
       23.80        21.37        40.41        44.09        30.05        25.87 
TCGA-TQ-A7RV TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A86M 
       61.41        43.20         7.89        20.02        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 
            22.420             20.055 
[1] "0.1 - 182.3 (22.4)" "0.0 - 211.2 (20.1)"
[1] "hr=" "1.9"
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    94 115
  19Q LOSS WILD-TYPE 134 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     94  115
  19Q LOSS WILD-TYPE  134  169
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               94                134
  MALE                115                169
[1] 2 2
[1] FALSE
D75V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   100  96
  19Q LOSS WILD-TYPE  84 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    100   96
  19Q LOSS WILD-TYPE   84  197
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO               100                 84
  YES               96                197
[1] 2 2
[1] FALSE
D75V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19Q LOSS MUTATED            23               44               142
  19Q LOSS WILD-TYPE         171               85                47
D75V6, multiclass
                   clus
vv                  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASTROCYTOMA                     23                171
  OLIGOASTROCYTOMA                44                 85
  OLIGODENDROGLIOMA              142                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                           9   190
  19Q LOSS WILD-TYPE                        12   282
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                       9                 12
  WHITE                                         190                282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    18 178
  19Q LOSS WILD-TYPE  14 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     18  178
  19Q LOSS WILD-TYPE   14  268
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   18                 14
  NOT HISPANIC OR LATINO              178                268
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     5   2
  20P LOSS WILD-TYPE 383 119
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                502 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                119 
$`20P LOSS MUTATED`
TCGA-DB-5277 TCGA-DU-8166 TCGA-E1-A7YH TCGA-FG-A87N TCGA-HT-7693 TCGA-S9-A89V 
       50.86        16.96        93.21        18.64        17.52        18.71 
TCGA-TQ-A7RM 
       36.69 

$`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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        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 
        2.40        11.47        62.96       156.23       154.36        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        33.27        29.85        31.69        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       26.17        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
       20.98        22.29        11.41        26.76        17.16        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       14.30        29.13         3.65        19.46        12.43        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU 
       21.30        23.90        75.02        51.88        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         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 
       52.21        36.82        18.77        14.93        42.54        41.33 
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 
       28.34        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        21.53        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-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-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10         2.96         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        56.58        13.45        41.49        45.60        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54         6.18 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55        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         7.99         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 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        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-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO 
       15.98         2.04        40.41        44.09        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        43.04        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        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 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             16.96               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             93.21             211.17 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            18.710             20.895 
[1] "17.0 - 93.2 (18.7)" "0.0 - 211.2 (20.9)"
[1] "hr=" "1.1"
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     5   2
  20P LOSS WILD-TYPE 223 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5    2
  20P LOSS WILD-TYPE  223  282
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                5                223
  MALE                  2                282
[1] 2 2
[1] FALSE
D76V4, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0   7
  20P LOSS WILD-TYPE 184 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    7
  20P LOSS WILD-TYPE  184  286
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                184
  YES                7                286
[1] 2 2
[1] FALSE
D76V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20P LOSS MUTATED             4                2                 1
  20P LOSS WILD-TYPE         190              127               188
D76V6, multiclass
                   clus
vv                  20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASTROCYTOMA                      4                190
  OLIGOASTROCYTOMA                 2                127
  OLIGODENDROGLIOMA                1                188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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     6
  20P LOSS WILD-TYPE                        21   466
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                 21
  WHITE                                           6                466
[1] 4 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     1   6
  20P LOSS WILD-TYPE  31 440
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    6
  20P LOSS WILD-TYPE   31  440
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 31
  NOT HISPANIC OR LATINO                6                440
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     2   1
  20Q LOSS WILD-TYPE 386 120
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                506 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                120 
$`20Q LOSS MUTATED`
TCGA-E1-A7YH TCGA-HT-A618 TCGA-TQ-A7RM 
       93.21        16.83        36.69 

$`20Q 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        46.95         7.56        49.94 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.12         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        91.13        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        63.88        46.06         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        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       31.69        24.43        26.17        24.99        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       21.57        95.11        20.98        22.29        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       17.16        21.30        17.98       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ 
       95.57       130.78        14.30        29.13         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ 
       12.43        16.18        21.30        23.90        75.02        51.88 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       15.32         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         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        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        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        21.53 
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        18.64         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-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-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-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
        1.81        16.14        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        56.58        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       41.49        45.60        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54         6.18        10.55        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         7.99         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         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        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        41.10        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       26.93        23.51        19.99        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       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 
       20.48        54.77        48.33        49.32        34.78        65.39 
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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       14.93        23.80        21.37        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       40.41        44.09        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       25.87        33.93        61.41        26.99        31.36        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF 
       43.20        13.51         0.10         7.89        39.16        20.02 
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 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             16.83               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             93.21             211.17 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             36.69              20.81 
[1] "16.8 - 93.2 (36.7)" "0.0 - 211.2 (20.8)"
[1] "hr=" "1.1"
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   0
  20Q LOSS WILD-TYPE 225 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE  225  284
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                3                225
  MALE                  0                284
[1] 2 2
[1] FALSE
D77V4, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   2
  20Q LOSS WILD-TYPE 183 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE  183  291
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 1                183
  YES                2                291
[1] 2 2
[1] FALSE
D77V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20Q LOSS MUTATED             2                1                 0
  20Q LOSS WILD-TYPE         192              128               189
D77V6, multiclass
                   clus
vv                  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASTROCYTOMA                      2                192
  OLIGOASTROCYTOMA                 1                128
  OLIGODENDROGLIOMA                0                189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     0
  20Q LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           0     3
  20Q LOSS WILD-TYPE                        21   469
D77V7, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       0                 21
  WHITE                                           3                469
[1] 4 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
  20Q LOSS MUTATED     1   2
  20Q LOSS WILD-TYPE  31 444
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE   31  444
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 31
  NOT HISPANIC OR LATINO                2                444
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    29   7
  21Q LOSS WILD-TYPE 359 114
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                36                473 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 7                114 
$`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        63.88        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        26.17        84.33        57.93 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YK TCGA-E1-A7Z4 TCGA-FG-7636 TCGA-FG-A60J 
       29.13        93.21        12.43       145.05        17.88        14.76 
TCGA-HT-7689 TCGA-HT-7857 TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8564 TCGA-HT-A61B 
       14.96         0.23        31.43         0.10        15.72        17.52 
TCGA-HW-7490 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A5F6 
       45.60         0.23         6.71         2.30         0.76         1.28 
TCGA-P5-A72W TCGA-P5-A77W TCGA-S9-A89Z TCGA-TM-A84Q TCGA-TQ-A7RR TCGA-VM-A8CF 
       10.42        19.20        20.48        25.38        25.87        20.02 

$`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        46.95         7.56        49.94        49.12 
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        91.13        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        46.06         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 
       23.21        17.46        13.71        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         2.40        11.47        62.96       156.23       154.36 
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        33.27        29.85        31.69        24.43        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76        17.16        21.30        17.98       139.04 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL 
       95.57       130.78        14.30         3.65        19.46        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU 
       21.30        23.90        75.02        51.88        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z6 
       32.45        36.82       146.14        13.08        73.48        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       39.48         0.23         0.20        47.77        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        42.54        41.33        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        28.34        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-A60K 
       38.27        10.72        18.38        18.71        23.70        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       21.53        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        18.64         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-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        31.69         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-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-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-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 
       56.58        13.45        41.49        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54         6.18        10.55        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-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A72U 
        7.99         2.37         4.11         5.88         7.63         0.23 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
        7.56        12.23         3.45         2.37         4.41        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        41.10        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       26.93        23.51        19.99        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       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 
       54.77        48.33        49.32        34.78        65.39        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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU 
       36.69        33.73        31.20        30.05        26.14        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        43.04        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        39.16        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 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            145.05             211.17 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            18.545             21.400 
[1] "0.1 - 145.1 (18.5)" "0.0 - 211.2 (21.4)"
[1] "hr=" "1"  
D78V2, continuous
D78V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    18  18
  21Q LOSS WILD-TYPE 210 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     18   18
  21Q LOSS WILD-TYPE  210  266
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               18                210
  MALE                 18                266
[1] 2 2
[1] FALSE
D78V4, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     9  23
  21Q LOSS WILD-TYPE 175 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      9   23
  21Q LOSS WILD-TYPE  175  270
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 9                175
  YES               23                270
[1] 2 2
[1] FALSE
D78V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  21Q LOSS MUTATED            23                7                 6
  21Q LOSS WILD-TYPE         171              122               183
D78V6, multiclass
                   clus
vv                  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASTROCYTOMA                     23                171
  OLIGOASTROCYTOMA                 7                122
  OLIGODENDROGLIOMA                6                183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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    35
  21Q LOSS WILD-TYPE                        21   437
D78V7, 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                 21
  WHITE                                          35                437
[1] 4 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
  21Q LOSS MUTATED     2  31
  21Q LOSS WILD-TYPE  30 415
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   31
  21Q LOSS WILD-TYPE   30  415
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 30
  NOT HISPANIC OR LATINO               31                415
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    30  27
  22Q LOSS WILD-TYPE 358  94
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                452 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                27                 94 
$`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 
       24.43        26.17        33.96        11.41        26.76        41.13 
TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YJ TCGA-E1-A7YM TCGA-E1-A7YS TCGA-E1-A7Z2 
      130.78        29.13        19.46        21.30        15.32        13.08 
TCGA-FG-7643 TCGA-FG-A4MY TCGA-HT-7477 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7690 
       20.09        23.70        24.26        42.74        31.69         0.10 
TCGA-HT-7860 TCGA-HT-A614 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-A5KK TCGA-P5-A5F6 
        0.49         2.70        16.14        16.83        12.76         1.28 
TCGA-P5-A72U TCGA-P5-A780 TCGA-QH-A6CS TCGA-RY-A83Z TCGA-S9-A6TS TCGA-S9-A6UA 
        0.23         2.37        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 
       26.93        20.02        18.71        20.48        40.64        26.99 
TCGA-VM-A8CD TCGA-VM-A8CF TCGA-WH-A86K 
        7.89        20.02        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 
       46.95         7.56        49.94        49.12         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        91.13        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        63.88        46.06         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        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5854 TCGA-DU-5855 
       13.71        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         2.40        11.47        62.96       154.36 
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        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       31.69        24.99        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       22.29        17.16        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         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-A7YD TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YL 
       95.57        14.30        93.21         3.65        12.43        16.18 
TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       23.90        75.02        51.88         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      146.14        73.48       145.05        32.35        39.48         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        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        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        28.34        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        21.53        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        18.64         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        56.58        13.45        41.49        45.60 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       68.32        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
        6.18        10.55        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         7.99         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-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R 
        7.56        12.23        19.20         3.45         4.41        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        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        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        19.99         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       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        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        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-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       61.41        31.36        43.04        43.20        13.51         0.10 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       39.16        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       51.06        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       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 
             19.33              21.40 
[1] "0.1 - 156.2 (19.3)" "0.0 - 211.2 (21.4)"
[1] "hr=" "3.1"
D79V2, continuous
D79V3, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    28  29
  22Q LOSS WILD-TYPE 200 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     28   29
  22Q LOSS WILD-TYPE  200  255
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               28                200
  MALE                 29                255
[1] 2 2
[1] FALSE
D79V4, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    13  39
  22Q LOSS WILD-TYPE 171 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     13   39
  22Q LOSS WILD-TYPE  171  254
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                13                171
  YES               39                254
[1] 2 2
[1] FALSE
D79V5, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  22Q LOSS MUTATED            29               11                17
  22Q LOSS WILD-TYPE         165              118               172
D79V6, multiclass
                   clus
vv                  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASTROCYTOMA                     29                165
  OLIGOASTROCYTOMA                11                118
  OLIGODENDROGLIOMA               17                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"
                    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                           2    54
  22Q LOSS WILD-TYPE                        19   418
D79V7, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       2                 19
  WHITE                                          54                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"
D79V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     2  50
  22Q LOSS WILD-TYPE  30 396
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   50
  22Q LOSS WILD-TYPE   30  396
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 30
  NOT HISPANIC OR LATINO               50                396
[1] 2 2
[1] FALSE

Clustering(80) Variable = XP LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    71  27
  XP LOSS WILD-TYPE 317  94
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               98               411 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               27                94 
$`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        13.71        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         2.40        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 
       31.69        22.29        21.30        17.98        57.93       134.27 
TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YK TCGA-E1-A7YS TCGA-E1-A7YV TCGA-EZ-7264 
      130.78        29.13        12.43        15.32        32.45        39.48 
TCGA-F6-A8O3 TCGA-FG-5964 TCGA-FG-7636 TCGA-FG-A4MY TCGA-FG-A6IZ TCGA-FG-A6J1 
        0.23        52.21        17.88        23.70        15.02        16.44 
TCGA-FG-A713 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7609 
       20.45        11.54         0.13         6.54        24.26        45.99 
TCGA-HT-7616 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-7857 
        0.23        14.96         0.10         2.96        19.23         0.23 
TCGA-HT-7902 TCGA-HT-8104 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A618 TCGA-HT-A61B 
       31.43        12.23        28.27        15.72        16.83        17.52 
TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-8321 TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EZ 
       68.32        40.01        42.54        19.00        14.40         2.30 
TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A780 
        1.28        10.42        11.64        12.23        19.20         2.37 
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        25.81        18.64         7.92        19.99        18.71 
TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A84I TCGA-TM-A84Q TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       20.48        49.32        28.08        25.38        40.41        44.09 
TCGA-TQ-A7RR TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8CD TCGA-VV-A829 TCGA-VV-A86M 
       25.87        26.99        31.36         7.89        37.05        16.01 
TCGA-WY-A858 TCGA-WY-A85B 
       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        46.95         7.56        49.94        49.12 
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 
       91.13        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        63.88        46.06         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        23.21        17.46 
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       154.36 
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        33.27        29.85 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       24.43        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 
       95.11        20.98        11.41        26.76        17.16       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5318 
        0.56        50.14        67.46        41.13        79.99        78.21 
TCGA-E1-5319 TCGA-E1-A7YD TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL 
       95.57        14.30        93.21         3.65        19.46        16.18 
TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YW 
       21.30        23.90        75.02        51.88         0.76        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-F6-A8O4 
      146.14        13.08        73.48       145.05        32.35         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       47.77        25.48        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       41.33        18.44        15.35        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       28.34        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-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       14.76        17.82        21.53        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       36.66        48.69        18.64         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        6.67        40.11         0.03        16.54         3.75        17.42 
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-7610 TCGA-HT-7611 TCGA-HT-7620 
       17.29         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-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10        31.69         0.10        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.48        39.09        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-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-A4DS 
        5.56        13.78         0.23        29.59        34.19         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-A619 
        5.33         2.70        16.93         1.81        16.14        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-7493 TCGA-HW-7495 
       56.58        13.45        41.49        45.60        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       39.75         6.18        10.55        12.76        20.81        20.71 
TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       42.77        14.40         0.23         6.71         7.99         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72X 
        4.11         5.88         7.63         0.76         0.23        13.25 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A77X 
       10.95         9.01        13.61         9.60         7.56         3.45 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU 
        4.41        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        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.14        35.38        36.82        24.39        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY 
       26.47        18.61        14.07        36.13        26.93        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        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       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        54.77        48.33        34.78        65.39 
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-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RM TCGA-TQ-A7RN 
       21.37        19.69        15.98         2.04        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-VM-A8C8 
       31.20        30.05        26.14        33.93        61.41        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       43.20        13.51         0.10        39.16        20.02        23.47 
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-A85C TCGA-WY-A85D TCGA-WY-A85E 
       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 
           19.215            21.400 
[1] "0.1 - 156.2 (19.2)" "0.0 - 211.2 (21.4)"
[1] "hr=" "1.3"
D80V2, continuous
D80V3, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    47  52
  XP LOSS WILD-TYPE 181 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     47   52
  XP LOSS WILD-TYPE  181  232
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              47               181
  MALE                52               232
[1] 2 2
[1] FALSE
D80V4, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    27  63
  XP LOSS WILD-TYPE 157 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     27   63
  XP LOSS WILD-TYPE  157  230
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               27               157
  YES              63               230
[1] 2 2
[1] FALSE
D80V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XP LOSS MUTATED            39               27                33
  XP LOSS WILD-TYPE         155              102               156
D80V6, multiclass
                   clus
vv                  XP LOSS MUTATED XP LOSS WILD-TYPE
  ASTROCYTOMA                    39               155
  OLIGOASTROCYTOMA               27               102
  OLIGODENDROGLIOMA              33               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           2    94
  XP LOSS WILD-TYPE                        19   378
D80V7, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      2                19
  WHITE                                         94               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"
D80V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    10  84
  XP LOSS WILD-TYPE  22 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     10   84
  XP LOSS WILD-TYPE   22  362
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                22
  NOT HISPANIC OR LATINO              84               362
[1] 2 2
[1] FALSE

Clustering(81) Variable = XQ LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    47  23
  XQ LOSS WILD-TYPE 341  98
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               70               439 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               23                98 
$`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         2.40 
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        22.29        21.30        17.98        50.14       134.27 
TCGA-E1-A7YE TCGA-E1-A7YK TCGA-E1-A7YS TCGA-E1-A7YV TCGA-EZ-7264 TCGA-F6-A8O3 
       29.13        12.43        15.32        32.45        39.48         0.23 
TCGA-FG-5964 TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7477 
       52.21        15.02        16.44        11.54         0.13        24.26 
TCGA-HT-7616 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-8104 TCGA-HT-8564 
        0.23         0.10         2.96        19.23        12.23        15.72 
TCGA-HT-A61B TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8321 TCGA-IK-7675 TCGA-KT-A74X 
       17.52        68.32        69.27        42.54        19.00        14.40 
TCGA-P5-A5EZ TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A737 TCGA-P5-A77W 
        2.30         1.28        10.42        11.64        12.23        19.20 
TCGA-QH-A65Z TCGA-QH-A6X4 TCGA-QH-A6X8 TCGA-RY-A83Z TCGA-S9-A6TV TCGA-S9-A6WP 
       14.04        14.53        16.73         9.90        18.77        18.64 
TCGA-S9-A7IS TCGA-S9-A7QW TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A84I 
        7.92        15.06        18.71        20.48        49.32        28.08 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8CD TCGA-VV-A829 
       26.99        31.36         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        46.95        49.94        49.12 
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        91.13 
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        63.88        46.06         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        23.21        17.46        13.71 
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       154.36        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        33.27        29.85        31.69 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       24.43        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 
       95.11        20.98        11.41        26.76        17.16       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 
        0.56        67.46        41.13        79.99        57.93        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
       95.57       130.78        14.30        93.21         3.65        19.46 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YN TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YU 
       16.18        21.30        23.90        75.02        51.88         0.76 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        32.35 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        47.77        25.48        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        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        28.34        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        21.53 
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 
       18.64         5.72        27.52         0.10         6.67        40.11 
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-7620 
        3.16        22.06        45.99        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-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-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        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-8105 
        9.40        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-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        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       13.45        41.49        45.60        35.44        39.75        40.01 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
        6.18        10.55        12.76        20.81        20.71        42.77 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
       14.40         0.23         6.71         7.99         2.37         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A730 
        5.88         7.63         0.76         0.23        13.25        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A77X TCGA-P5-A780 
        9.01        13.61         9.60         7.56         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS 
        4.41        15.16         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-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       10.29        16.34         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-A6TS 
        5.46        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        41.10        28.14        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ 
       84.99        31.10        19.86        26.47        18.61        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
       36.13        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        20.68        18.54        28.37        27.16       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        54.77 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       48.33        34.78        65.39        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-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CF 
       43.04        43.20        13.51         0.10        39.16        20.02 
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 

  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 
            18.00             22.06 
[1] "0.1 - 134.3 (18.0)" "0.0 - 211.2 (22.1)"
[1] "hr=" "1.9"
D81V2, continuous
D81V3, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    29  42
  XQ LOSS WILD-TYPE 199 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     29   42
  XQ LOSS WILD-TYPE  199  242
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              29               199
  MALE                42               242
[1] 2 2
[1] FALSE
D81V4, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    18  45
  XQ LOSS WILD-TYPE 166 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     18   45
  XQ LOSS WILD-TYPE  166  248
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               18               166
  YES              45               248
[1] 2 2
[1] FALSE
D81V5, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XQ LOSS MUTATED            26               16                29
  XQ LOSS WILD-TYPE         168              113               160
D81V6, multiclass
                   clus
vv                  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASTROCYTOMA                    26               168
  OLIGOASTROCYTOMA               16               113
  OLIGODENDROGLIOMA              29               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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                           1    68
  XQ LOSS WILD-TYPE                        20   404
D81V7, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 7
  BLACK OR AFRICAN AMERICAN                      1                20
  WHITE                                         68               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"
D81V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4  64
  XQ LOSS WILD-TYPE  28 382
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4   64
  XQ LOSS WILD-TYPE   28  382
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                28
  NOT HISPANIC OR LATINO              64               382
[1] 2 2
[1] FALSE
